5
Evaluating Mississippi River Water Quality

Accurate evaluation of Mississippi River quality, and how that water quality changes over time, is important for several reasons. This information is essential in measuring the effectiveness of water quality remediation strategies such as Total Maximum Daily Loads (TMDLs). It also is central to determining if water quality standards are being met. More generally, knowledge of water quality in a river or a watershed often is of great interest to citizens, elected officials, and decision makers. Comprehensive and accurate portrayal of water quality conditions requires both the collection of data (monitoring) and an understanding of the system that is supported by scientific investigations (research). Ideally there will be clear and mutually supportive links between monitoring and research. Effective data gathering efforts also require a sustained commitment over time if water quality trends are to be detected and evaluated.

Monitoring and evaluating Mississippi River water quality poses unique challenges because (1) monitoring efforts face logistical difficulties and hazards in some parts of the river system; (2) processes and natural fluctuations in the Mississippi River operate on scales of decades and over hundreds of miles; (3) the river spans, or forms, boundaries of political units or jurisdictions that have differing priorities and resources; and (4) water quality standards and environmental conditions vary across the entire system. For example, because of natural, longitudinal changes in water quality from upstream to downstream, levels of suspended sediment and turbidity that would be considered “pristine” (i.e., pre-settlement) in the lower reaches of the Mississippi River would be considered objectionable and indicative of severe degradation if encountered in the river’s headwaters. Likewise, because of natural patterns and differences along the river’s length, water



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5 Evaluating Mississippi River Water Quality A ccurate evaluation of Mississippi River quality, and how that water quality changes over time, is important for several reasons. This information is essential in measuring the effectiveness of water qual- ity remediation strategies such as Total Maximum Daily Loads (TMDLs). It also is central to determining if water quality standards are being met. More generally, knowledge of water quality in a river or a watershed often is of great interest to citizens, elected officials, and decision makers. Com- prehensive and accurate portrayal of water quality conditions requires both the collection of data (monitoring) and an understanding of the system that is supported by scientific investigations (research). Ideally there will be clear and mutually supportive links between monitoring and research. Effective data gathering efforts also require a sustained commitment over time if water quality trends are to be detected and evaluated. Monitoring and evaluating Mississippi River water quality poses unique challenges because (1) monitoring efforts face logistical difficulties and haz- ards in some parts of the river system; (2) processes and natural fluctuations in the Mississippi River operate on scales of decades and over hundreds of miles; (3) the river spans, or forms, boundaries of political units or juris- dictions that have differing priorities and resources; and (4) water quality standards and environmental conditions vary across the entire system. For example, because of natural, longitudinal changes in water quality from upstream to downstream, levels of suspended sediment and turbidity that would be considered “pristine” (i.e., pre-settlement) in the lower reaches of the Mississippi River would be considered objectionable and indicative of severe degradation if encountered in the river’s headwaters. Likewise, because of natural patterns and differences along the river’s length, water 

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 EVALUATING MISSISSIPPI RIVER WATER QUALITY quality conditions (e.g., turbidity, temperature, dissolved oxygen) that ex- ist in the headwaters can never be realized in the far downstream reaches. Beyond typical longitudinal patterns, there are also large differences among the subbasins within the Mississippi drainage basin. Any comprehensive evaluation of Mississippi River water quality must consider these differences along the river’s length and across the river’s watershed. This chapter examines issues associated with evaluating Mississippi River water quality. It describes some key features of the river and how its hydrologic and watershed characteristics affect water quality monitoring. The chapter reviews past and existing monitoring programs on the Mis- sissippi River mainstem. It discusses the value of river system monitoring in tracking changes in water quality and the importance of monitoring in achieving Clean Water Act goals. It also discusses challenges of using data and information from monitoring programs to help meet Clean Water Act objectives. Finally, this chapter offers recommendations for enhanced state and federal efforts to improve monitoring efficiency, reduce data gaps, and strengthen implementation of the Clean Water Act. MISSISSIPPI RIVER BASIN STRUCTURE, HYDROLOGY, AND MONITORING The mainstem Mississippi River exhibits markedly different hydrology, sediment loads, and other features between its upstream and downstream portions. These upstream-downstream differences are driven in large part by inputs from the Mississippi’s two main tributaries, the Missouri and Ohio Rivers, which enter the Mississippi at St. Louis, Missouri, and Cairo, Illinois, respectively. The Missouri River is the longest tributary of the Mississippi, and its flow is about two-thirds of the upper Mississippi River above St. Louis. It carries a suspended sediment load several times that of the upper Mississippi River (Meade, 1995). The dams constructed on the Missouri River have reduced the Missouri’s total sediment contribution to the Mississippi by more than half since 1953 (Meade and Parker, 1985; Meade et al., 1990). As the Mississippi flows southward, the waters it re- ceives from the Illinois and Missouri Rivers more than double its discharge (Meade, 1995). Downstream, the Ohio River is the Mississippi’s largest tributary with respect to discharge, carrying almost twice the discharge of the upper Mississippi River above St. Louis (Table 2-1). Just as the river’s discharge doubles when it receives the waters of the Missouri, its discharge more than doubles again as it receives the waters of the Ohio River (Meade, 1995). Downstream of the Mississippi River’s confluence with the Ohio River, the river takes on a very different character than in its upstream reaches. In the Mississippi’s lower reaches, the river becomes much deeper and wider

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0 MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT and in many areas contains swiftly moving, swirling, and turbulent water. Author John Barry provides a colorful depiction of lower Mississippi River hydraulics in his 1997 book, Rising Tide: The complexity of the Mississippi exceeds that of nearly all other riv- ers. Not only is it acted upon; it acts. It generates its own internal forces through its size, its sediment load, its depth, variations in its bottom, its ability to cave in the riverbank and slide sideways for miles, and even tidal influences, which affect it as far north as Baton Rouge. Engineering theories and techniques that apply to other rivers, even such major rivers as the Po, the Rhine, the Missouri, and even the upper Mississippi, simply do not work on the lower Mississippi, which normally runs far deeper and carries far more water. Monitoring efforts in the river’s lower stretches are difficult and hazardous even under relatively calm conditions. These physical differences between the upper and lower Mississippi River influence the ability of the states along the river to monitor water quality and help explain some of the differences in water quality monitoring efforts among the 10 Mississippi River states. Downstream of Cairo, the influence of direct lateral inputs (i.e., from the adjoining bank or inflowing tributaries) to the Mississippi mainstem becomes relatively less important. In the lower river, water quality thus primarily is a function of upstream inputs, with less influence from the im- mediately adjacent land. The states of the lower river thus understandably consider the river’s condition, and possible water quality remedies, to be largely beyond their control and responsibility. For example, the Mississippi River and its basin upstream of Memphis, Tennessee, represent 80 percent of the total drainage area, 76 percent of the total flow volume, and more than 90 percent of the total riverbank miles for the entire system (Leopold et al., 1964). A consequence of the structure of the Mississippi River drainage sys- tem is that the water quality in the mainstem of the lower river, because of the large and relatively slowly changing mass of water involved, remains relatively constant between those points at which major tributaries join the flow. Thus, closely spaced sampling along the longitudinal axis of the channel generally is not needed to get an accurate measure of average river and water quality conditions over relatively large areas. However, because inflowing tributaries may take many miles to mix completely with the main body of the river, lateral and vertical patterns in water quality can be sub- stantial and persistent. As the following sections explain, the influences of the spatially variable Mississippi River drainage structure on water quality have contributed to differences in U.S. federal and state monitoring of the river and in how states along the river have approached Mississippi River water quality monitoring.

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 EVALUATING MISSISSIPPI RIVER WATER QUALITY FEDERAL AND REGIONAL MISSISSIPPI RIVER EVALUATIONS As on many of the nation’s large rivers, various types of monitoring have long been conducted on the Mississippi River. River flows have been measured, water quality has been sampled, and ecosystem changes have been tracked. The sum of these monitoring efforts presents a complex and fragmented picture because they have been conducted by different federal and state agencies and scientists, at differing spatial scales and time inter- vals, with differing objectives, and with varied and changing budgets. Since monitoring efforts are conducted at differing scales and for differing objec- tives, there is no “one-size-fits-all” or standard river monitoring program. Monitoring system designs and programs must consider and balance a need for stability and continuity, on the one hand, with changes in sci- entific paradigms, monitoring technologies and instrumentation, budgets, and political and management objectives on the other. They must cope also with the reality that it is not practical or feasible to monitor continuously every site of interest in the system at hand (e.g., a large river) and that such systems will always contain complexities and unknowns. Scientists must gather and analyze enough information to improve scientific understand- ing, while recognizing that there are limits to the amount of data that can be gathered and there always will be some uncertainties regarding the state and dynamics of large water systems or ecosystems. To help cope with these realities, models of the system(s) being monitored are often developed so data gathered from individual sites can be used to construct a quantitative or conceptual framework of system-wide dynamics and behavior. Federal Monitoring Programs Federal agencies have sponsored and conducted the large-scale moni- toring efforts for the Mississippi River. One of today’s prominent river mon- itoring efforts is the Long Term Resource Monitoring Program (LTRMP). Established in 1986 as part of the U.S. Army Corps of Engineers’ Envi- ronmental Management Program (EMP) for the upper Mississippi River, this initiative seeks to supply essential scientific information to the EMP for the purposes of maintaining the upper Mississippi River as a viable large river ecosystem with multiple uses (USGS, 1999). Since the LTRMP’s inception, the Environmental Management Technical Center (EMTC) has implemented the program. The EMTC today is part of the Upper Midwest Environmental Sciences Center, which is a U.S. Geological Survey (USGS) science center. The USGS, the U.S. Fish and Wildlife Service, and the five upper Mississippi River basin states are cooperative partners in the EMP, with the Corps of Engineers responsible for programmatic and financial oversight. The LTRMP samples biota and water quality in five mainstem

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 MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT FIGURE 5-1 Long Term Resource Monitoring Program study areas (1993-2006). SOURCE: USGS (1999). Figure 5-1 reaches upstream of the Ohio River confluence to represent conditions and habitat on the upper Mississippi River system (Figure 5-1). In each LTRMP study reach, several hundred locations have been sampled for biota and water quality since 1993 (Soballe and Fischer, 2004). The LTRMP-EMP is- sued a comprehensive report in 1999 on upper Mississippi River ecological status and trends. The report was described as “a milestone in the history of the LTRMP. For the first time, data collected since the start of the LTRMP are summarized in one report alongside historical observations and other scientific findings” (USGS, 1999).

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 EVALUATING MISSISSIPPI RIVER WATER QUALITY In addition to its efforts within the LTRMP, the USGS has been a leader in other Mississippi River monitoring efforts, both in river flows and in water quality sampling. USGS efforts in measuring discharge on the Mis- sissippi River mainstem have remained relatively constant over the years, but there has been a decrease in the extent of its water quality monitoring efforts. For example, at its peak in the 1970s, the National Stream Quality Accounting Network (NASQAN), operated by the USGS, provided exten- sive coverage of the nation’s rivers, including the Mississippi. However, that network has been steadily diminished in the number of sites, the number of samples, and the number of parameters collected, and no other national monitoring programs or monitoring by states and other entities has replaced it. NASQAN data have been useful for several different applications and computations. For example, USGS NASQAN data can be used to compute long-term trends in the monthly nutrient flux at St. Francisville, Louisiana (see Goolsby et al., 1999). Figure 5-2 shows changes in the number of active FIGURE 5-2 History of active NASQAN sites at the national level. Reductions in the network that were implemented in the late 1990s, and again in 2001, left only four or five sites active on the Mississippi River mainstem (Clinton, Iowa; Grafton, Ill.; Thebes, Ill.; and St. Francisville, Figure 5-2 La.). SOURCE: Alexander et al. (1997).

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 MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT NASQAN sites from 1973 to 1995, and Figure 5-3 shows active NASQAN sites across the United States as of 2000. The USGS implemented the National Water Quality Assessment (NAWQA) network in 1991, just as much of the NASQAN network was being eliminated (USGS, 2007). However, the NAWQA program does not represent a full replacement for NASQAN with regard to large riv- ers. Although NAWQA includes many Mississippi River tributaries, it includes no mainstem sites downstream of Lake Pepin. As a result, today only a few mainstem water quality sites remain in the USGS network downstream of Lake Pepin. These stations are at Clinton, Iowa; Grafton, Illinois; Thebes, Illinois; and St. Francisville, Louisiana. The NASQAN site on the Atchafalaya River at Melville, Louisiana, also could be in- cluded in this group because the Atchafalaya is the Mississippi River’s primary distributary in the Mississippi’s lower reaches (see Figure 5-3). Although some monitoring sites have been lost, a monitoring station at Belle Chasse, Louisiana, has come back online, and the USGS intends to bring another Atchafalaya River station online. The loss of monitoring sites of course represents the loss of future data from an individual site. However, a greater concern with the loss of water quality monitoring sta- FIGURE 5-3 Active NASQAN stations as of 2000. SOURCE: USGS (2006). Figure 5-3

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 EVALUATING MISSISSIPPI RIVER WATER QUALITY tions is that large-scale assessments, which could be useful in addressing regional or basinwide water management issues (e.g., hypoxia), cannot be replicated because more recent data from the same area have not been collected. Comprehensive Mississippi River Assessments Two widely cited water quality assessments that examine the Missis- sippi River at a regional or system-wide scale were published in 1995 and in 1999, and were headed by USGS scientists Robert Meade (1995) and by Donald Goolsby (Goolsby et al., 1999), respectively (these two reports are cited extensively in Chapter 2). In the 1995 report, the Meade team as- sessed water quality conditions along the Mississippi River mainstem from Minneapolis to New Orleans. They conducted longitudinal sampling on seven dates from 1987 to 1990 between St. Louis and New Orleans and on three additional dates from 1991 to 1992 between Minneapolis and New Orleans. Results from the 1995 Meade study were used by the Goolsby team as part of six reports that supported a Mississippi River assessment. Although these two USGS studies are a rich source of data in terms of both quality and quantity, they do not provide the coverage in space (many ar- eas were unsampled) and time (these were snapshots or annual averages) needed to detect the frequency and duration of water quality standard violations for the Section 303(d) and Section 305(b) biennial assessments of the river required by the Clean Water Act (CWA). Furthermore, it is unlikely that these assessments can be repeated in the foreseeable future. Similarly, the 1999 USGS status and trends report for the upper Missis- sippi River, although a useful and creative synopsis of upper river ecology, is not Clean Water Act specific. That is, it is not aimed at determining if designated uses along the river are being met or assessing the frequency and duration of violations of water quality standards. There have been other assessments of water quality along select por- tions of the river in addition to these studies. A 2002 report of water quality changes and conditions in the upper river near the Twin Cities is an excel- lent example (see Stoddard et al., 2002). However, no other studies have attempted to evaluate and characterize the entire river like the reports from the Meade and Goolsby teams. The limited amount of water quality and river ecosystem data inhibits evaluations of lower Mississippi River water quality. The USGS conducts some sampling between Cairo and New Orleans, but this entails consider- able difficulty, risk, and expense and therefore is very limited. Tennessee has conducted only modest data collection efforts, most of which are from the mainstem river directly downstream of Memphis. Arkansas, Kentucky, and Mississippi generally conduct minimal or no water quality sampling

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 MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT in the Mississippi River mainstem. Louisiana State University and the Louisiana Department of Environmental Quality have conducted more Mississippi River water quality sampling and have compiled their results into assessments. There is a greater abundance of Mississippi River water quality data for the upper Mississippi River than for the lower river, due in part to ef- forts both of the federal-state EMP and LTRMP and of some upper river states. Through its NASQAN and NAWQA programs, the USGS has col- lected some water quality data for the Mississippi River, but these efforts have not been systematic and sustained, they have not been directed toward Clean Water Act objectives, and the resources allocated to these programs generally have declined over time. As the following section explains, the majority of water quality monitoring efforts along the Mississippi River aimed specifically at Clean Water Act directives have been conducted at the state level. MONITORING ASSOCIATED WITH CLEAN WATER ACT OBJECTIVES Monitoring and other techniques that determine whether water qual- ity standards are met, including water quality and designated uses, are key steps toward achieving the Clean Water Act’s “fishable and swimmable” objectives. Because states have the lead in implementing the Clean Water Act, monitoring and the design of monitoring programs are state, not federal, responsibilities. The Clean Water Act does not include any specific monitoring requirements, such as frequency of monitoring, parameters to be monitored, or locations for the siting of monitoring stations. Water Quality Monitoring in an Interstate Setting Several court decisions involving TMDL development have expressly refused to require the U.S. Environmental Protection Agency (EPA) to con- duct water quality monitoring (Sierra Club . Hankinson, 939 F. Supp. 865, 870 (N.D. Ga. 1996); Ala Center for the En’t . Reilly, 796 F. Supp. 1374, 1380 (W.D. Wash. 1992), aff’d 20 F.3d981, 987 (9th Cir. 1994)). Others have found no legal mandate in the Clean Water Act for adequate state monitoring prior to EPA action to approve or disapprove a list of impaired waters that require TMDLs (Friends of the Wild Swan, Inc. . EPA, 130 F. Supp. 2d 1184, 1193 (D. Mont. 1999); Sierra Club . EPA, 162 F. Supp. 2d 406, 413 n.5 and 416 (D. Md. 2001)). At the same time, however, Clean Water Act Section 106(e)(1) conditions state receipt of federal grant funds for water pollution control programs on the EPA’s finding that the state is monitoring the quality of its surface waters and compiling and analyzing the data obtained.

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 EVALUATING MISSISSIPPI RIVER WATER QUALITY Water quality monitoring performed to meet Clean Water Act objec- tives has some recognized deficiencies, and some reports have confirmed the need to improve substantially the conduct of water quality monitoring, in both quantity and quality, as an essential basis for credible water qual- ity improvement programs (NACEPT, 1998; GAO, 2000a; NRC, 2001; NAPA, 2002). For example, an EPA report commenting on state programs noted (USEPA, 2003c): States have taken very different approaches, within their resource limita- tions, to implement their monitoring programs. They have applied a range of monitoring and assessment approaches (e.g., water chemistry, sediment chemistry, biological monitoring) to varying degrees, both spatially and temporally, and at varying levels of sampling effort. It is not uncommon for the reported quality of a water body (i.e. attainment or nonattainment) to differ on either side of a state boundary. Although some differences can be attributed to differences in water quality standards, variations in data collection, assessment methods, and relative representativeness of the available data contribute more to differences in assessment findings. These differences adversely affect the credibility of environmental management programs. Moreover, the discipline and practice of water quality monitoring does not always perfectly match CWA-related monitoring requirements. Water qual- ity monitoring techniques and practices also are constantly being updated and improved (see Box 5-1). Interstate waters such as the Mississippi River pose significant problems for the Clean Water Act framework. In addition to the size of such systems, political boundaries can create jurisdictional complications and make it dif- ficult for individual states to commit resources to water quality monitoring in such waters. Moreover, given the Mississippi River’s interstate nature, some states assume or assert that the monitoring and the condition of the river are exclusively federal responsibilities. A statement in the Mississippi Section 303(d) report for 2006 (MDEQ, 2006b) provides an example: The Mississippi Department of Environmental Quality (MDEQ) is not listing the Mississippi River on MDEQ’s Mississippi 2006 § 303(d) list. In previous lists, the MDEQ included various segments of the river, but not based on data. Because any TMDL or delisting decision deals with mul- tiple states and multiple EPA Regions, the MDEQ considers this a national issue. EPA Region 4 and Region 6 would jointly develop any TMDL for the Mississippi River. At the national level, the EPA compiles the Section 305(b) assessments from each state into a national synthesis that is intended to indicate the con- dition of the nation’s waters. In concept, at least, a similar approach could be used to assess the entire Mississippi River. There are, however, shortcom- ings with this approach, especially as it pertains to interstate rivers and to

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 MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT BOX 5-1 What Is Water Quality Assessment? Under the Clean Water Act, water quality assessments are technical reviews of physical-chemical, bacteriological, biological, and/or toxicological data and infor- mation to determine the quality of a state’s surface water resources. Assessment begins with the assignment of appropriate designated uses for waterbodies and measurable water quality criteria that can be used to determine use attainment (http://www.epa.gov/waterscience/standards/about/uses.htm). The criteria, which may include biological, chemical, and physical measures, define the types of data to be collected and assessed. The EPA Office of Water has developed national indicators for surface waters and a conceptual framework for using environmen- tal information in decision making (http://www.epa.gov/waterscience/standards /about/crit.htm). In the more traditional approach to water quality assessment, monitoring data are compared to water quality criteria in order to make decisions on whether a waterbody is supporting (or not) its designated uses, such as aquatic life support, water contact recreation, and drinking water. This involves comparing criteria on a parameter-by-parameter basis. Basic limitations of this approach are (1) mea- surement of a set of individual physical, chemical, and biological parameters at numerous points in an aquatic system is expensive; (2) measurements often are available for only a few parameters; and (3) relating a set of parameter measure- ments to the health of an aquatic system is often difficult. A newer, faster, and less expensive water quality assessment approach, which has emerged over the last two decades, is the use of rapid biological surveys, or rapid bioassessment protocols (RBPs). This approach is a response, in part, to dwindling resources available for monitoring efforts. It is also an attempt to evaluate biological conditions rapidly and the effects of water quality on those conditions in a particular system. In the RBP approach, surveys are conducted of aquatic macroinvertebrates, fish, or periphyton, and the presence or absence and relative abundance of species found is used to develop a numeric index that can be compared to a rating scale. This approach requires calibration to specific geographic area and, for the assessment of large rivers, is still in early stages of development. Whichever assessment approach is used, a determination is made of whether the waterbody is fully supporting all of its uses; if not, the waterbody is consid- ered impaired. The causes and sources of the impairment are then determined. Impaired waters are subject to further monitoring and are listed on the state’s Impaired Waters List. The EPA has national guidance on assessing and listing im- paired waters, known as the Consolidated Assessment and Listing Methodology (CALM), which generally undergoes revisions for each biennial reporting cycle. an assessment at a regional or national scale. In particular, there is no sci- entifically defensible (i.e., statistical) basis for combining and extrapolating Section 305(b) assessments of individual waterbodies or reaches to make a quantitative statement about the extent, frequency, or fraction of compli- ance or noncompliance on a system-wide, regional, or national scale.

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 MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT BOX 5-2 Mississippi River Monitoring and Fish Consumption Advisories A primary motivator of state-conducted monitoring of the Mississippi River is the protection of fish resources and maintenance of up-to-date fish consumption advisories. In fact, the issue of fish contamination is one of the greatest concerns of sport and commercial fishermen and the general public along the upper Missis- sippi River. Many commercial and recreational anglers depend heavily on Missis- sippi River fishery resources, and many regional and local community economies are supported by recreational use and river-related tourism. Fisheries are jeopardized when toxins contaminate fish by direct exposure to water or sediments or through the food chain. Some of these contaminants are legacy materials (e.g., PCBs [polychlorinated biphenyls], DDT [dichlorodiphenyl- trichloroethane]) and some derive from current practices (e.g., mercury, dioxin, lead). These toxins can accumulate in fish tissue over time and reach concentra- tions that pose a risk to human health. Concentrations of toxic substances in fish tissue can be much higher than those found in the water. States along the river monitor various fish species and use different ap- proaches for assessing health risks. The states publish Fish Consumption Adviso- ries (FCAs) that recommend limits on the consumption of fish, and they decide if a river segment should be listed as impaired under the Clean Water Act because of this contamination. Along some segments of the river, bordering states have issued different FCAs and have categorized the impairment of the river section differently. This can lead to public confusion about the risks from fish caught in the river and can have economic and regulatory implications for point source dis- chargers to the river (FTN Associates, Ltd. and Wenck Associates, Inc., 2005). Evaluations of fish tissue quality differ from traditional water quality assess- ment, which involves measurement of a particular water quality parameter and comparing it to a criterion. Fish tissue analysis provides an aggregate measure of aquatic organism exposure to a range of contaminants. Such analyses are used in water quality impairment assessments and also support public health protection through issuance of FCAs. The FCA process starts with collection and analysis of fish tissue, proceeds to an evaluation of the risk to human health, and then estimates what consumption limit (e.g., frequency and amount) should be recommended for specific users (e.g., children, pregnant women) of specific fish types (e.g., fish species, size, body portions) taken from specific areas. If fish contaminants exceed a certain level or a FCA is issued for a waterbody, the river segment may be added to the Clean Water Act Section 303(d) list of impaired waterbodies. The states, District of Columbia, U.S. territories, tribes, and local governments have primary responsibilities for protecting their residents from the potential health risks from eating contaminated fish caught in local waters. The states have de- veloped their own fish advisory programs over the years, and there are variations among them in terms of extent of monitoring, frequency of sampling, decisions made regarding advisories, and so on. EPA plays a role in providing a National Listing of Fish Advisories database. This is an annual compendium of information on locally issued fish advisories and safe eating guidelines that is provided to EPA by the states and other bodies. EPA has compiled and made this information available since 1993 (available online at http://www.epa.gov/waterscience/fish/ advisories/2006/index.html#basic).

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 EVALUATING MISSISSIPPI RIVER WATER QUALITY Mississippi River in its Section 305(b) assessments and Section 303(d) lists. Differing combinations of data sources are used to evaluate each of Iowa’s 14 upper Mississippi River reaches (UMRBA, 2004). With the possible exception of Louisiana, monitoring downstream of the Ohio River confluence that is related to Clean Water Act assessment, enforcement, and restoration is less active than in the upper Mississippi River states. In general, the lower Mississippi River states consider Mis- sissippi River water quality to be the responsibility of others and give it low priority for monitoring funds. For example, Mississippi and Arkansas provide an example of limited involvement in Mississippi River monitor- ing, because they no longer assess the Mississippi mainstem as part of their Section 305(b) process. STATUS OF AND PROSPECTS FOR MISSISSIPPI RIVER MONITORING Current Efforts The status of monitoring on the Mississippi River to obtain data rel- evant to Clean Water Act assessment and enforcement presents a mixed picture. Assessment of water quality and habitat for the Clean Water Act has been done relatively well on the upper river, but even there, there are limitations within the data gathered to date. Furthermore, levels of com- mitment of the 10 Mississippi River states to river monitoring are varied and may change in the future. Data collected often are not readily com- parable (Box 5-3). Federal monitoring programs on the Mississippi River are focused on fish and wildlife populations, habitat conditions, and mass transport of nutrients and sediments. These programs are not designed to be part of CWA-related monitoring (e.g., verifying whether a given state’s designated uses are being attained). The limitations of federal monitoring programs on the Mississippi River are illustrated within the upper Mississippi River LTRMP. This pro- gram has the primary purpose of monitoring biotic conditions and habitat at a system-wide, multiyear scale. The water quality data collected by this program are a primary source of information for substantial portions of the upper river, and although it has been useful in Clean Water Act assessments (e.g., by Minnesota), the LTRMP is focused on habitat conditions and is not intended to track compliance with water quality standards. Thus, the program does not monitor a host of pollutants that have numeric standards and are priority pollutants of regulatory interest under the Clean Water Act, nor does LTRMP monitoring lend itself to the detection of short-term, acute conditions (e.g., violations of water quality standards) at specific locations for specific durations or frequencies. Further, this program, like many other

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 MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT BOX 5-3 Consistency of Water Quality Data The ability to combine or compare data from different sources is an important issue with no easy solution. Data can differ not only because of differing methods or equipment used to collect and analyze water samples, but also because of differences in sampling design (i.e., what basic aspects of the system are repre- sented in the data; see Soballe, 1998). For example, data that are collected during midday sampling must be adjusted before they can be combined or compared with data from a program that samples only at night or during pre-dawn hours. Such an adjustment may not be possible. Likewise, data that are collected only to represent high-flow storm conditions in one location may not be easily com- bined or compared with data that sample end-of-pipe or low-flow conditions in another. An approach often used in stream sampling programs is to collect a “flow- weighted” sample in which a single sample is generated for chemical analysis by adding water to a single container for several hours or several days in proportion to the river’s surface elevation or flow. Such a sample is useful for calculating mass transport, particularly during a single rainstorm or flood; however, results of this flow integration are not readily comparable to those produced by sampling at regular, longer-term intervals (weeks or months) to detect extremes or to estimate average conditions. There is no single standard method that can be applied to all sampling to meet all information needs. federally sponsored efforts, has been reduced since the late 1990s and has been forced to focus more closely on its primary mission of tracking the status of biota and habitat in specific study areas. Although the LTRMP has collected data from thousands of locations along the river for more than 15 years, these efforts have tended to be seasonal and limited to five river reaches. There has been no mechanism to extrapolate these data to inter- vening portions of the river or to other periods of time. Data collected by the program clearly have value for improved understanding of Mississippi River aquatic ecosystems (see, for example, USGS, 1999), but they have limited utility regarding CWA-related assessment of the entire system. The seemingly low level of Clean Water Act-related monitoring on por- tions of the Mississippi River is not unique or even unusual. For example, the GAO reported that as of 1996, states assessed only 19 percent of their rivers and streams (GAO, 2000a). The GAO also noted that states tend to focus monitoring on those waters with suspected pollution problems in order to direct scarce resources to areas that could pose the greatest risk (GAO, 2000a). Because of the dilution capacity of the Mississippi River, the difficulty of large-river water quality monitoring, and the absence of

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 EVALUATING MISSISSIPPI RIVER WATER QUALITY sole responsibility of individual states for its quality, states have given Mis- sissippi River monitoring low priority. A wide range of water quality and ecosystem monitoring efforts have been and continue to be conducted along the Mississippi River. These ef- forts are quite variable in spatial and temporal implementation, are not well coordinated, and for the most part are not designed for Clean Water Act assessment purposes. Better coordination and a shared sense of purpose and value of monitoring information among the mainstem river states are needed for more effective and useful system-wide monitoring. The Value and Importance of Monitoring Monitoring of Mississippi River water quality has not been performed in a system-wide manner for extended periods (e.g., decades) and at inter- vals of time (e.g., monthly) or space (in every major reach) that would sup- port rigorous assessment of water quality and ecology for the river. As this chapter has discussed, there are considerable challenges to conducting this type of extensive monitoring: large-river sampling methods and instrumen- tation need to be standardized; states and federal agencies must compare and cooperate on sampling and monitoring strategies to make the most of their expenditures and prevent duplication of ongoing efforts; the resources required for extensive and sustained monitoring can be considerable; and there are practical challenges to monitoring, especially in the often danger- ous lower Mississippi River. Despite the costs and analytical and logistical challenges involved in creating such a program, there are also costs in not having a systematic monitoring program for the entire Mississippi River and into the Gulf of Mexico. The nation’s rivers, including the Mississippi, have realized im- provements in some aspects of water quality as a result of the Clean Water Act. Many of those improvements have been achieved through reductions in point source discharges of pollutants. Water quality issues and problems of primary concern along the river today are different than in the early 1970s when the Clean Water Act was enacted and consist primarily of nonpoint pollutant loads from agricultural, urban, and suburban activities. The framework within the Clean Water Act for addressing nonpoint source pollutants relies more strongly on scientific data, monitoring, and modeling of water quality than on an end-of-pipe approach to treating point source pollution (Box 5-4 discusses the role of modeling in water quality assessments). Rather than focusing on reducing discharge from individual sites, contemporary programs for achieving water quality improvements in the Mississippi River and the Gulf of Mexico must encompass pollutant inputs from across the entire watershed. They must also monitor water quality conditions for the river as a whole, not just at

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 MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT BOX 5-4 Role of Modeling in Water Quality Assessment Although acquisition and analysis of monitoring data is the approach preferred by the EPA for identifying impaired waters, modeling can have an important supplementary role. Integrated monitoring and modeling can often provide bet- ter information than monitoring alone for the same total cost (NRC, 2001). For example, Section 303(d) and related guidance from EPA recommend focusing efforts on waterbodies or segments that are suspected of violating water quality standards. Such targeted monitoring represents the use of available information regarding water quality impairments to guide monitoring toward particular sites. A potentially valuable use of modeling in relation to Section 303(d) listings would be to formalize the use of available information on impairment probability in monitor- ing system design. Limited monitoring resources could be focused on sites where impairment is most uncertain, thus improving the efficiency of monitoring. points near specific sources of effluent. Today, water quality improvements rely more heavily on a science- and data-intensive approach to understand- ing the linkages between activities that generate pollutant loads and their ultimate impacts on waterbodies. Without comprehensive monitoring of a river system, it is difficult to understand trends in water quality conditions, to realize the impacts of watershed-focused programs designed to reduce nutrient and sediment loads, and to determine whether designated uses are being achieved. Beyond limited amounts of data, another challenge to system-wide as- sessment is that some of the data collected by the many state and federal monitoring programs have fundamental differences in their underlying purposes and designs (Box 5-4). When monitoring program details are compared, it is often discovered that data from different sources cannot be combined in a meaningful way. Thus, the ability to compare data over large scales of time and space is further restricted. The situation is created, in part, by the scales of time and space required for adequate research and monitoring and by the specific issues the monitoring system is designed to address. These scales are dictated by natural scales of the system and the questions being addressed (Soballe, 1998), and the questions and issues have seldom been the same across multiple monitoring programs. For the Mississippi River, the lack of a coordinated water quality data gathering program and of a centralized water quality information system hinders effective implementation of the Clean Water Act and acts as a barrier to maintaining or improving water quality along the river and in the Gulf of Mexico. The EPA should take the lead in establishing such a program. In doing so, it should work closely with the 10 Mississippi River

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 EVALUATING MISSISSIPPI RIVER WATER QUALITY mainstem states and with federal agencies with relevant expertise and data, such as the Corps of Engineers, the USGS, and the National Oceanic and Atmospheric Administration (NOAA). Part of this effort should focus on collecting data necessary to develop numeric water quality standards for nutrients in the Mississippi River and the Gulf of Mexico. Emerging Monitoring Challenges Some emerging developments in aquatic system monitoring pose partic- ular challenges for implementation in large systems such as the Mississippi River. There is increasing interest in biological monitoring because of the direct link to ecosystem health and the potential to evaluate the aggregate impact of water pollution. Techniques and biocriteria have been developed for smaller streams, but neither have been established yet for large rivers. There also have been advances in tracking sources of sediment inputs to streams. Biomonitoring In many Clean Water Act assessments, the condition of a waterbody with respect to supporting a designated aquatic life use is evaluated pri- marily through stream biological community assessments. Biomonitoring of resident biota can often be conducted more quickly and less expensively than monitoring of physical-chemical water quality parameters. Bioassess- ment protocols (e.g., rapid bioassessment protocols; see Box 5-5) could fill some data gaps with regard to the Mississippi River CWA-related assess- ments, but this approach has been limited to date to wadable streams. In addition, meaningful biocriteria (numeric measures of desirable fish popula- tions, etc.) for large rivers have not been established, nor have means been developed to readily collect the necessary data for sound bioassessments of large rivers. Impairments for human contact or consumption can also be assessed using fish tissue analyses and evaluations of raw (intake) water monitored by water purveyors. These are used in some reaches of the Mississippi mainstem, but their application seems to be less than consistent (UMRBA, 2004). Recreational use impairments are often based on bacteriological data, such as fecal coliform counts, and these are commonly used, at least in the upper river. Sediment Monitoring Sediment concentration and transport are crucial water quality and river ecology issues along the entire Mississippi River, but systematic monitoring

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0 MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT BOX 5-5 Rapid Bioassessment Protocols Biological surveys and other direct measurements of the resident biota in sur- face waters are often used to determine whether a surface waterbody is meeting a designated aquatic life use. The Rapid Bioassessment Protocols (Barbour et al., 1999) were developed in the 1980s and 1990s by various states and compiled by the EPA in a guidance document. The guidance includes protocols for three types of aquatic life—periphyton, benthic macroinvertebrates, and fish—as well as for habitat assessment. These protocols have all been tested in streams and wadable rivers in various parts of the United States. They have been used as rapid, inexpensive means of water quality assessment and have been utilized extensively by states in development of Section 305(b) water quality inventories. Bioassessment has also been used in Section 303(d) impairment assessments. Effects of excess nutrients, sediments, and other pollutant classes can be readily identified. Bioassessment protocols that are practicable and can be linked unequivocally and quantitatively to the functional health (or biotic integrity) of the large river are still under development. A limitation of the use of bioassessments for evaluating conditions in large rivers such as the Mississippi River is the difficulty in linking biological metrics unambiguously to specific causal factors. Thus, it currently is not possible to initiate specific remedial action or management based on the numeri- cal value of bioassessment indices alone. However, these indices can be valuable for identifying the need for a more detailed evaluation of conditions in impaired locations. of these important variables poses analytical and conceptual challenges. Standard, widely accepted approaches to assessing sediment dynamics (i.e., deposition and resuspension) have not been developed and accurate mea- surements of sediment dynamics over long time periods (years) and large spatial scales (tens to hundreds of kilometers) are difficult to obtain. For example, reports on Mississippi River water quality and ecological integrity often note sediment, “siltation,” and turbidity as priority concerns in the upper river (UMRBA, 2004; Headwaters Group, 2005). These various terms are interrelated and, although sometimes used interchangeably, do not have the same meaning. Monitoring data for any one of these characteristics are not particularly informative about the others. Turbidity, for example, is governed by the size, composition, and concentration of suspended particles in the water. It can be viewed as a short-term, near-field property because the particles that create this phenomenon may change rapidly (minutes) over short distances (meters) in the river. Monitoring that does not cap- ture these short-term, near-field variations may not reveal the extremes of

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 EVALUATING MISSISSIPPI RIVER WATER QUALITY turbidity to which river biota are exposed. Smaller particles (fine silts and clays) have the greatest influence on turbidity, but coarser particles (sand) usually dominate the process of sedimentation. In contrast to turbidity, sedimentation is a longer-term processes (years to centuries), and assess- ment of this phenomenon depends on the scales of space and time used in the measurement. Moreover, the data used to study these processes on the river generally are sparse (see Box 5-6). As Figure 5-6 illustrates, an area that appears to be accumulating sedi- ment for several years or decades may be deeply scoured by occasional large floods and therefore be in dynamic balance over the longer term. Likewise, one portion of a river reach may be accumulating sediment, while an adja- cent zone is being scoured, so that on a larger spatial scale, the total reach appears to be in balance. However, this balance may be only temporary and extend over a few years or a few decades. These complications and variations over time regarding sediment trans- port and loadings are illustrative of the larger challenges that attend ac- curate and consistent monitoring of water quality variables and provide background for the following conclusions regarding federal and state water quality monitoring programs along the Mississippi River. BOX 5-6 Sediment Transport and Deposition: A Monitoring Challenge A study of one of the upper Mississippi’s tributary streams—Coon Creek, in Wisconsin—demonstrates some of the complex patterns of sediment transport and deposition in a single stream, how those patterns may change over time (Fig- ure 5-6), and the kind of monitoring needed to study long-term sediment transport and deposition. Research in Coon Creek has shown that sediment yield varies depending on where it is measured within a basin. Despite a significant decrease of sediment flux within the basin caused by improved land management practices, sediment yield from Coon Creek to the Mississippi River has held fairly constant (at least according to available data). As indicated, this continued flow of sediment is coming from upstream channels and banks. There is presently only one sediment measuring station in this entire region for tributaries to the Mississippi River. However, measurements on the main river downstream at Dubuque, Iowa, indicate that sediment transport is presently only about half the rate existing in the 1940s (Pannell, 1999). How can this apparent disparity be explained? Are either or both measures wrong? There simply are not enough sediment measuring stations to know.

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 MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT FIGURE 5-6 Sediment budgets for Coon Creek, Wisconsin, 1853-1993. Numbers are annual averages for the periods in thousand tons per year. All values are direct Figure 5-6 measurements except “net upland sheet and rill erosion,” which is the sum of all sinks and the efflux (sediment yield to the Mississippi River) minus measured sources. The lower main valley and tributaries are sediment sinks, whereas the up- per main valley is a sediment source. SOURCE: Reprinted, with permission, from Trimble (1999). © 1999 by the Ameri- can Association for the Advancement of Science.

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 EVALUATING MISSISSIPPI RIVER WATER QUALITY SUMMARY Restoration and maintenance of water quality and related ecosystem conditions in the Mississippi River require understanding of current system conditions and trends over time. Monitoring data are necessary for the assessment and planning required under the Clean Water Act to maintain and improve water quality. However, large rivers such as the Mississippi are difficult to monitor consistently and comprehensively for water quality and biota. High-quality monitoring programs require expensive and rugged equipment, specially trained personnel, and more time in the field than is needed to monitor streams and small rivers. Further exacerbating the chal- lenge of assessment of the Mississippi River is the fact that water quality and habitat differ across the river’s many subbasins. Along the Mississippi River, there are large longitudinal gradients in water quality, geomorphol- ogy, and biota. There is no consistency in the amount and quality of water quality data available for the length of the mainstem Mississippi River. Some areas in the upper river have been relatively well monitored and there is a large amount of water quality data. At the federal level, these efforts primarily are rep- resented by the EMP and LTRMP. Data from the LTRMP could be useful in a supplementary role in Clean Water Act assessments, but the LTRMP is focused on habitat conditions and is not intended to track compliance with water quality regulations. The USGS also has collected some Missis- sippi River water quality data via its NASQAN and NAWQA programs, but these efforts have not been systematic and sustained, they have not been directed toward Clean Water Act objectives, and the resources allocated to the programs have generally declined over time. On the upper river, Minnesota, Illinois, and Wisconsin have promoted the most extensive Mississippi River programs at the state level, although the resources devoted to these programs have varied over time. In the lower river states, there are fewer data and there have been far fewer monitoring initiatives. Tennessee has conducted only modest data collection efforts, most of which are on the mainstem river directly downstream of Memphis. Arkansas, Kentucky, and Mississippi generally conduct minimal or no wa- ter quality sampling in the Mississippi River mainstem. Louisiana has con- ducted more Mississippi River water quality sampling and has conducted some assessments with the results. Some of these upstream-downstream differences are driven by different values and uses of the respective portions of the river; the physical difficulties and hazards posed by monitoring in the large lower Mississippi River also are factors. Water quality monitoring along the Mississippi River mainstem is in- consistent over both space and time. The extent to which Mississippi River mainstem states monitor water quality in the river varies considerably,

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 MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT and these efforts lack coordination. States along the river have assigned different designated uses to the same river segments; they use different judgments and methods in their assessments; and there is no standard for the time frame or frequency of water quality monitoring. Mississippi River monitoring programs conducted by the USGS and the Corps of Engineers have diminished over time in many places, although the USGS is increas- ing monitoring capabilities and the number of stations in some areas (e.g., Atchafalaya River). Generally speaking, the extent and quality of biologi- cal, physical, and chemical data along the river generally do not support thorough CWA-related assessments. The lack of a centralized Mississippi River water quality information system and data gathering program hin- ders effective application of the Clean Water Act and acts as a barrier to maintaining and improving water quality along the Mississippi River and into the northern Gulf of Mexico. States along the mainstem Mississippi River, together with the federal government, need to coordinate better with respect to planning monitoring activities and sharing the data that result. In a climate of ever-decreasing resources for monitoring, all federal and state agencies involved in moni- toring the Mississippi River mainstem should cooperate and coordinate their efforts to the greatest extent possible. The Mississippi River clearly is of federal interest because of the many states in the river basin, the river’s prominent role in supporting interstate commerce, and its hydrologic and ecological systems that extend across several states and into the Gulf of Mexico. The federal government should take the lead in ensuring adequate water quality monitoring, a cornerstone of effective Clean Water Act imple- mentation along the Mississippi River and into the Gulf of Mexico. There is a clear need for federal leadership in system-wide monitoring of the Mississippi River. The EPA should take the lead in establishing a water quality data sharing system for the length of the Mississippi River. This would include establishing coordinated monitoring designs and de- veloping mechanisms (hardware, software, and protocols) necessary for efficient data sharing among monitoring and resource agencies and Section 305(b) and Section 303(d) assessment teams. It also would entail ensuring consistency in river monitoring in terms of parameters measured, units and methods employed, and siting of monitoring stations along the length of the river. The EPA should draw on the considerable expertise and data held by the U.S. Army Corps of Engineers and the USGS, as well as NOAA and the water-related data for the northern Gulf of Mexico that it collects and maintains. The EPA should work closely with Mississippi River states in establishing this plan and system. A priority for EPA in this regard should be to coordinate with the states to ensure the collection of data necessary to develop numeric water quality standards for nutrients in the Mississippi River and the Gulf of Mexico.