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An Introduction to Instream Flow Science and Programs

In the simplest terms, instream flow is the water flowing in a stream channel (IFC, 2002). This simple concept belies the difficulty of determining what that flow should be among competing uses for water, such as irrigation, public supply, recreation, hydropower, and aquatic habitat. The simple definition may not account for variations in flow levels across different seasons and wet, dry, and normal years. A challenge facing natural resource managers is to find a workable balance among these demands and use appropriate methods to quantify instream flow needs for each of these uses. Instream flow programs were created to meet this challenge.

An instream flow recommendation will give a numerical answer to the question, “How much water should be in the river?” Instream flow programs help water managers meet management goals of biology, municipal water supply, or water quality considerations. The Instream Flow Council (IFC) offers this definition for instream flows (IFC, 2002):

The objective of an instream flow prescription should be to mimic the natural flow regime as closely as possible. Flow regimes must also address instream and out-of-stream needs and integrate biotic and abiotic processes. For these reasons, inter-and intra-annual instream flow prescriptions are needed to preserve the ecological health of a river.

Two primary literature sources describe instream flow science, Instream Flows for Riverine Resource Stewardship (IFC, 2002) and Rivers for Life: Managing Water for People and Nature (Postel and Richter, 2003). These books are based on instream flow research and studies conducted on many rivers in North America and the rest of the world and reference hundreds of citations. Information in these books, as well as other primary and secondary references, is used as a foundation for some of the conclusions and recommendations in this report.

This chapter offers a brief tutorial on the basic structure of instream flow science, studies, and programs. Trends and principles in the science



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The Science of Instream Flows: A Review of the Texas Instream Flow Program 3 An Introduction to Instream Flow Science and Programs In the simplest terms, instream flow is the water flowing in a stream channel (IFC, 2002). This simple concept belies the difficulty of determining what that flow should be among competing uses for water, such as irrigation, public supply, recreation, hydropower, and aquatic habitat. The simple definition may not account for variations in flow levels across different seasons and wet, dry, and normal years. A challenge facing natural resource managers is to find a workable balance among these demands and use appropriate methods to quantify instream flow needs for each of these uses. Instream flow programs were created to meet this challenge. An instream flow recommendation will give a numerical answer to the question, “How much water should be in the river?” Instream flow programs help water managers meet management goals of biology, municipal water supply, or water quality considerations. The Instream Flow Council (IFC) offers this definition for instream flows (IFC, 2002): The objective of an instream flow prescription should be to mimic the natural flow regime as closely as possible. Flow regimes must also address instream and out-of-stream needs and integrate biotic and abiotic processes. For these reasons, inter-and intra-annual instream flow prescriptions are needed to preserve the ecological health of a river. Two primary literature sources describe instream flow science, Instream Flows for Riverine Resource Stewardship (IFC, 2002) and Rivers for Life: Managing Water for People and Nature (Postel and Richter, 2003). These books are based on instream flow research and studies conducted on many rivers in North America and the rest of the world and reference hundreds of citations. Information in these books, as well as other primary and secondary references, is used as a foundation for some of the conclusions and recommendations in this report. This chapter offers a brief tutorial on the basic structure of instream flow science, studies, and programs. Trends and principles in the science

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The Science of Instream Flows: A Review of the Texas Instream Flow Program are discussed, major components of an instream flow program are described, and current Texas methods for defining instream flow requirements are briefly reviewed. The chapter ends with three examples of current or recent instream flow efforts that use a number of the instream flow components, and research needs for the continued evolution of the science. TRENDS AND PRINCIPLES OF INSTREAM FLOW SCIENCE Trends in Instream Flow Science In the United States, the National Environmental Policy Act (NEPA) of 1969 required federal planning activities to “create and maintain conditions under which man and nature can exist in productive harmony, and fulfill the social, economic, and other requirements of present and future generations…” This purpose of NEPA is reflected in many instream flow studies that seek balance among competing uses of water. Instream flow science began to develop in the years after NEPA in the late 1960s and 1970s, and continues to evolve today. Over these decades, four trends and seven principles mark the trajectory of instream flow science growth. • Hydrology and Hydraulics. The convention of instream flow science is changing from developing a single, minimum flow or “flat-line” flow to a range of flows that account for seasonal and inter-annual variation, magnitude, timing, frequency, and rate of change (IFC, 2002; Poff et al., 1997; Postel and Richter, 2003). These hydrologic attributes translate into different levels of flow: subsistence flows, base flows, high flow pulses, and over bank flows (Figure 3-1). This range of flows is referred to as a flow regime. Subsistence flow is the minimum streamflow needed during critical drought periods to maintain tolerable water quality conditions and to pro vide minimal aquatic habitat space for the survival of aquatic organisms. Base flow is the "normal" flow conditions found in a river in between storms, and base flows provide adequate habitat for the support of diverse, native aquatic communities and maintain ground water levels to support riparian vegetation. High flow pulses are short-duration, high flows within the stream channel that occur during or immediately following a storm event; they flush fine sediment deposits and waste products, restore normal water quality following prolonged low flows, and provide longitudinal connectivity for species movement along the river. Lastly, overbank

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The Science of Instream Flows: A Review of the Texas Instream Flow Program flowis an infrequent, high flow event that breaches riverbanks. Overbank flows can drastically restructure the channel and floodplain, recharge groundwater tables, deliver nutrients to riparian vegetation, and connect the channel with floodplain habitats that provide additional food for aquatic organisms. Increasingly, instream flow science promotes the inclusion of one or more of these flows in an instream flow study. • Biology. The biological component of instream flows once focused on flow needs for one species (usually fish) and sometimes only one life stage of one species. Although single species remain the center of many instream flow evaluations, instream flow and riverine scientists now recognize and strive to account for multiple riverine ecosystem functions, sustained aquatic and riparian communities, and adequate habitat in instream flow programs (Calow and Petts, 1992, 1994). FIGURE 3-1 Daily streamflow hydrograph for Guadalupe River at Victoria, TX, with base flows, subsistence flows, high flow pulses, and overbank flows identified. SOURCE: Data from USGS Gage No. 08176500, water year 2000.

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The Science of Instream Flows: A Review of the Texas Instream Flow Program • Geomorphology. The stream channel used to be the spatial limit of instream flow work. Current goals, however, for state-of-the-art instream flow studies have expanded the spatial scope to include physical processes in the stream channel, riparian, and floodplain areas. • Disciplinary Focus. In the 1960s and 1970s, hydrologists alone established the flow requirements primarily from hydrologic statistics (Orsborne and Allman, 1976). Increasingly, instream flow interdisciplinary teams have scientists from related fields of biology, geomorphology, water chemistry and quality, and water law and policy, as well as hydrology and hydraulics. The challenge of instream flow work is to develop an instream flow program that balances instream flow science(s), public values, and legal mandates. A multi-disciplinary team is best equipped to achieve and maintain this balance. These four trends have made instream flow studies more comprehensive, but difficulties still exist for conducting instream flow studies. First, these trends result in studies that are more resource-intensive to conduct. Many times agencies simply do not have the staff, time, and monetary resources required to conduct this type of comprehensive instream flow study. And second, these more comprehensive instream flow considerations may further complicate the process of integrating results from disparate studies into a single flow recommendation. Still, the science is new and these obstacles, too, may be overcome with more research, information, and communication. Principles of Instream Flow Science There are several principles of effective instream flow programs included in the IFC’s Instream Flows for Riverine Resource Stewardship (2002) and Postel and Richter (2003). The following list is adapted from these sources. These principles are reflected in the components of a state-of-the-art instream flow program and echo the four trends of instream flow science. Preserve whole functioning ecosystems rather than focus on single species. Mimic, to the extent possible, the natural flow regime, including seasonal and inter-annual variability (Figure 3-1). Expand the spatial scope of instream flow studies beyond the river channel to include the riparian corridor and floodplain systems.

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The Science of Instream Flows: A Review of the Texas Instream Flow Program Conduct studies using an interdisciplinary approach. Instream flow studies need hydrologists, biologists, geomorphologists, and water quality experts all working together. Experts can come from academia, public, and private sectors. Use reconnaissance information to guide choices from among a variety of tools and approaches for technical evaluations in particular river systems (see IFC, 2002 and Table 3-1). Practice adaptive management, an approach for recommending adjustments to operational plans in the event that objectives are not being achieved (TPWD, TCEQ, and TWDB, 2003). Involve stakeholders in the process. The first three of these principles emphasize actions that should be conducted: preserve whole ecosystems, simulate the natural flow regime, and include floodplain and riparian zones in instream flow considerations. The last four principles offer means to accomplish the first three: take an inter- and multi-disciplinary approach; use a variety of tools; practice adaptive management; and involve stakeholders. Together, these seven principles reflect the scientific trends in instream flow science and provide the foundation for the components of state-of-the-art instream flow programs and studies. COMPONENTS OF AN INSTREAM FLOW PROGRAM Instream flow programs involve technical and non-technical components. Technical elements are the areas in which empirical or modeling evaluations are conducted: hydrology and hydraulics, biology, geomorphology and physical processes, water quality, and connectivity. Legal, regulatory, and public participation issues are some non-technical components of an instream flow program. Both technical and non-technical components are important in a state-of-the-art-instream flow program; otherwise, untenable situations can occur. For example, the most scientifically valid instream flow recommendation will not be implemented if it violates a permitting process, is out of compliance with water quality regulation, or lacks public support in the river basin. A successful instream flow recommendation will embody the seven principles and have clear goals, stakeholder involvement and support, technical evaluations, appropriate modeling approaches, integration of the various components, and adaptive management (IFC, 2002; Postel and Richter, 2003). Each component is briefly introduced below.

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The Science of Instream Flows: A Review of the Texas Instream Flow Program Clear Goals Goals are statements of the activities or functions that instream flows are intended to support or achieve. Establishing clear management goals and objectives is an important component of any viable instream flow activity. River management personnel allocate stream resources among a variety of uses such as water supply, recreation, irrigation, and aquatic habitat protection. A lack of clear goals can create confusion as management agencies try to resolve competing demands or implement policy changes. Problems stemming from a lack of clarity in management objectives and authorities have been noted in several NRC reports of river systems across the United States, including the Colorado River (NRC, 1999), the Missouri River (NRC, 2002a), and the Upper Mississippi River (NRC, 2004b). Ultimately, the act of setting goals for a program is a political action. In the case of instream flows, a heavy emphasis is on science, but the policy makers determine the parameters and focus of the instream flow program. Scientists subsequently carry out the technical evaluations accordant with these goals, and therefore need to play a strong role in setting the goals. The role of good science is to provide sound information that is useful in a forum for discussion by stakeholders and agency decision makers. Scientific input is critical to ensure that policy goals are consistent with scientific feasibility and that progress towards achieving the goals can be documented with measurable criteria. Stakeholder Involvement The IFC recognizes that public involvement and support are critical elements of instream flow programs (IFC, 2002). Several types of public involvement opportunities exist in an instream flow program: outreach and education, public hearings and meetings, and working groups. Stakeholder input can occur at several stages in an instream flow program. The public can participate in authorizing legislation, setting goals, and approving or commenting on instream flow recommendations. Public involvement can increase support for an instream flow program, and the benefits of public support for instream flow protection outweighs the costs of involving the public in the process (IFC, 2002; Postel and Richter, 2003).

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The Science of Instream Flows: A Review of the Texas Instream Flow Program Technical Evaluations Technical evaluations are the sampling and modeling pieces of an instream flow study. These are often the heart of an instream flow study and consume the most resources. Technical evaluations of hydrology and hydraulics, biology, physical processes, and water quality involve empirical sampling or quantitative modeling. Connectivity involves the connections among and transfers between these aspects. In the best instream flow work, technical evaluations are closely aligned with the program and study goals. This alignment increases efficient uses of resources. Hydrology and Hydraulics Hydrology is potentially the most critical element of instream flow studies and has been considered the "master variable" because the biology, physical processes, and water quality components directly relate to it (Poff et al., 1997). Hydrology is used to assess hydraulic functions, water quality factors, channel maintenance and riparian forming processes, and physical habitat for target aquatic species. A flow regime encompasses the seasonality and periodicity of various types of flows, such as subsistence flows, base flows, high flow pulses, and overbank flows (Figure 3-1). Hydrologic/hydraulic technical evaluations aim to understand and quantify the magnitude, frequency, timing and duration of subsistence, base, high pulse, and overbank flows; the degree to which the natural flow regime has been altered; descriptive aspects of the hydrologic system, such as location of springs, tributaries, and dams; and impacts of land and water use on the flow regime. Other examples of questions to be addressed in hydrologic/hydraulic technical evaluations are listed in Table 3-1. Biology Until recently, biology components in many instream flow prescriptions targeted one, or at best a few, important game or commercial species. Now, however, many new programs try to focus on whole riverine ecosystems. An instream flow biologic evaluation will assay fish species as well as invertebrates, amphibians, reptiles, birds, mammals, and riparian plants that are dependent on the river corridor for some portion of their life cycles. Depth, velocity, substrate, and/or instream cover constitute hydraulic habitat in aquatic systems, which is often emphasized in instream flow studies. Suitable hydraulic habitat is necessary, but it is not the only

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The Science of Instream Flows: A Review of the Texas Instream Flow Program factor that affects the health of an aquatic ecosystem. Other factors that must also be considered include reproductive success of various species, disease outbreaks, predation, and competition for food. Biological technical evaluations are often the main focus of instream flow studies, as habitat, life stages, or population dynamics are frequently the purpose of the study. Ecosystem processes can be difficult to measure or model, and biological sampling can be extensive in attempts to be comprehensive. To avoid wasting resources, biological technical evaluations should be tailored to the goals of the instream flow study and conducted in ways that are applicable to flow conditions. For example, aspects of biological instream flow sampling may refer to flow regime impacts on habitat, species of concern, or assemblages and life stages of species. Other sample questions for biological technical evaluations are listed in Table 3-1. Geomorphology and Physical Processes Physical processes form and maintain the shape of the stream channel and floodplain. The form of a river channel results from interactions among discharge, sediment supply, sediment size, channel width, depth, velocity, slope, and roughness of channel materials (Knighton, 1998; Leopold et al., 1964). The floodplain and riparian zone are also shaped by sediment transport and deposition. Stream channels react to changes in sediment dynamics and either degrade or aggrade along the longitudinal gradient in response to sediment load. Channel form provides the physical structure for habitat for aquatic organisms. Human modifications such as channelization and bank fortification impact the channel form and habitat. Instream flow technical evaluations of physical processes may document changes in channel structure, aquatic habitat composition, riparian vegetation, and other effects of physical processes in river systems. Other subjects of physical processes technical evaluations are listed in Table 3-1. Water Quality The primary assays of water quality in most instream flow studies are sediment and total suspended solids (TSS), nutrients, dissolved oxygen, and temperature. Temperature influences a variety of life history strategies of aquatic organisms and can impact fish migration, timing of spawning, length and success of egg incubation, growth rates, feeding behavior, or susceptibility to disease and parasites. Most aquatic organisms require

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The Science of Instream Flows: A Review of the Texas Instream Flow Program moderate to high levels of dissolved oxygen, and the amount of dissolved oxygen affects biota in different ways, as different aquatic species can be highly tolerant or intolerant of low dissolved oxygen levels. Nutrient loadings to a stream can cause low levels of dissolved oxygen which can have deleterious effects on quantity and quality of habitat for macroinvertebrates and fish. Fine sediment and other suspended solids have well documented, negative effects on aquatic systems and represent a major source of degraded water quality in receiving waters throughout the United Sates (Waters, 1995). Water quality issues are regulated at the Federal level by the Environmental Protection Agency and at state levels by agencies such as the Texas Commission on Environmental Quality (TCEQ). Water quality is not always included in instream flow programs because in many circumstances, the agency that administers water quality does not have jurisdiction over water quantity issues. However, water quality is relevant to instream flow efforts because water quality is highly dependent on water quantity and instream flows, and water quality technical evaluations should seek to highlight these connections. Sample questions that indicate connections between water quality and biological aspects and hydrologic/hydraulic aspects are listed in Table 3-1. TABLE 3-1 Sample Questions to Guide Technical Evaluations Technical Components of an Instream Flow Program Suggested Questions for Technical Evaluations Hydrology/Hydraulics Available data Are the available hydrologic data sufficient for assessing the hydrologic conditions? Should monitoring be instituted where known deficiencies exist? Which statistical methods and tools (e.g., regionalization, record augmentation, disaggregation, etc.) can be utilized to develop needed data? Flow regime Are the available streamflow data sufficient to characterize annual and seasonal flow variability including the probability of floods or droughts? What is known about the magnitude, frequency, timing, and duration of base flows, subsistence flows, high flow pulses, and overbank flows? Should historical streamflow data be divided into pre- and post-development data sets? To what degree has the natural flow regime been altered? Hydrologic system Where are the major tributaries, major springs, dams, and diversions (including groundwater withdrawal) that influence the spatial pattern of flow? Is there longitudinal (upstream to downstream) connectivity in flow or are there major discontinuities (i.e., diversion dams), and if so where? What are the topographic and roughness

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The Science of Instream Flows: A Review of the Texas Instream Flow Program   conditions of the channel and floodplain? What are the stage-discharge relationships from nearby gaging stations? What are the statistical characteristics of streamflows? Land and water use What is known about the flow regime at key points in the watershed? What activities (e.g., trends in land use and surface water withdrawal, etc.) are influencing the flow regime and what are future projections for these trends? How do dam and reservoir operations impact flow regime and what are future projections for these operations? Biology Available data Are data from pre-project monitoring efforts available? Flow regime What is the importance of drought, flooding and intermediate flow conditions (flow variability) to habitat? What are the important connections to reservoirs or floodplains? Species of concern What species (fish, birds, mammals, invertebrates, aquatic plants or riparian vegetation) are of greatest concern from either ecological or socioeconomic stand-points? What times of year are most critical for these species? Assemblages and life stages of species Will modifications to current or naturalized flows protect habitat for the most flow-sensitive species or life-stages? Are flows sequenced to support life stages? Physical Processes Geomorphic system How do morphology and physical processes of the channel and floodplain vary spatially within the study area? Is the channel and floodplain system in dynamic equilibrium or disequilibrium? If the channel is a state of disequilibrium, what flow management scenarios could lead to a new equilibrium condition? Is the sediment input to each segment in equilibrium with the capacity of the channel to transport it through the segment? Is control of sediment input necessary? Geomorphology and aquatic ecology links How do physical habitat characteristics vary spatially? What physical features and processes provide key habitat for aquatic or riparian organisms of interest? What are current trends linking geomorphology and aquatic and riparian ecology? Can trends be reversed towards more naturalized conditions? Land and water use Has human activity and land use significantly altered the stream channel and floodplain morphology and processes? Do these alterations have a negative impact on key habitat? If so, what human activities are associated with this alteration? Are lateral channel migration, avul-

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The Science of Instream Flows: A Review of the Texas Instream Flow Program   sion, or meander cutoff processes important in this system, and have these processes been inhibited by flow alteration or other human activities? Water Quality Available data What is the present water quality status of the river segment? Are any of its designated uses impaired? If so, has a total maximum daily load (TMDL) study been done, and what are its results? Where are the wastewater discharge permit locations on the segment? What are their permitted flows? What proportion of the summer low flows in the river arises from upstream wastewater discharges? What is the current dissolved oxygen (DO) profile along the river? Has this changed appreciably in recent years? What is the stream temperature profile along the river? How does it change diurnally and seasonally? What is the total suspended solids concentration in the river? How does it change with discharge? How are water quality components affected by flow characteristics during the year and between different years? Species of concern What water quality components are of greatest concern to the target organisms, life stages, or riverine processes (DO, suspended sediment, temperature, chemical elements, nutrients)? Is the species distribution affected by water pollution (a typical consequence of polluted waters is a significant reduction in species diversity and an increase in pollutant tolerant species)? Land and water use Do land management activities affect water quality? If so, how do they affect riverine processes and organisms? Do opportunities (short- and long-term) exist to manage water quality-related factors in the watershed? Spatial variability Do water quality characteristics vary along the river, its tributaries, lakes, and estuaries (if any) throughout the watershed? If so, how do they change? Are these variations important? Connectivity Connectivity is “the flow, exchange, and pathways that move organisms, energy, and matter through river systems” (IFC, 2002). An instream flow evaluation should consider connections among hydrologic, biologic, geomorphic, and chemical aspects of instream flow. Examples of important connections are floodplain development processes, transfer of mass and energy from upstream to downstream positions, and vertical connections between surface and groundwater processes. Typical barriers to con-

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The Science of Instream Flows: A Review of the Texas Instream Flow Program TABLE 3-3 Ordination of Some Basic Biological Assessment Methodologies from Holistic to Specific  

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The Science of Instream Flows: A Review of the Texas Instream Flow Program FIGURE 3-2 Example integrated hydrograph based on building blocks of subsistence, base, high flow pulses, and overbank flows. flow depletion (typically expressed as percentages of the natural flow) during different water year types. This approach is particularly useful in river basins in which much of the natural flow volume and seasonal patterning remains and instream flow goals aim to mimic the natural ecosystem character. Although integration of the technical pieces leads to the quantitative flow recommendation, the integration phase should also account for legal, institutional and/or socioeconomic issues that may influence the implementation of the instream flow recommendation. A number of formal analytical methods that might be applied to integrate social, economic, and legal considerations are available (see Kraft and Furlong, 2004). Stakeholder input and involvement are also important to provide insight to the local social and economic manifestations of the flow recommendation. Adaptive Management Adaptive management is widely recognized as a powerful approach to manage complex and dynamic situations (NRC, 2004c). Adaptive management is sometimes referred to as “learning by doing” and it is driven

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The Science of Instream Flows: A Review of the Texas Instream Flow Program FIGURE 3-3 Example hydrograph based on the percent of flows approach for the Peace River in Florida. by the goals of the program (Postel and Richter, 2003). There are five iterative steps to adaptive management in instream flow work: (1) develop goals; (2) develop or revise conceptual model; (3) develop or revise the flow prescription; (4) implement strategies for restoring flows; and (5) monitor and assess attainment of goals (Postel and Richter, 2003). Ideally, instream flow programs are long-term enterprises that take several years to establish and additional years to incorporate the necessary study iteration and monitoring. Adaptive management is particularly useful in such studies, as it can test (and revise as necessary) the initial implementation of an instream flow program, assess ecological responses to new flow regimes, and add flexibility to the program and methods in the event that goals are not achieved. Therefore, a commitment to long- term monitoring, and anticipation that methods and flow recommendations may need revision over several years, are hallmarks of an adaptable instream flow program. INSTREAM FLOW EXAMPLES Many state instream flow programs have been in place for years. However, few of them provide much more than minimum levels of base flow

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The Science of Instream Flows: A Review of the Texas Instream Flow Program protection and fewer still have validated flow prescriptions empirically. A state-of-the-art instream flow program takes time and resources to design and implement. Three examples of instream flow approaches are presented. The first example is a recount of the existing methods used in Texas to define instream flow requirements. The last two are more recent studies that highlight one or more state-of- the-art components. The Savannah River example (Georgia and South Carolina) shows the benefits of stakeholder involvement in the processes of developing goals and establishing instream flows. The Instream Flow Study of the Lower Colorado Basin (Texas) illustrates the utility of “critical flows” in determining instream flow recommendations. Existing Methods for Defining Instream Flow Requirements in Texas Texas currently has two hydrologic methods for defining instream flow requirements; one for water permitting (Lyons method) and the other for water planning (Consensus Criteria for Environmental Flow Needs, CCEFN). The Lyons method was developed by a fisheries biologist at the Texas Parks and Wildlife Department (TPWD), Barry W. Lyons (Bounds and Lyons, 1979). The approach uses percentages by month of daily-averaged flows (see IFC, 2002; Tennant, 1976) as the parameter that determines instream flows in Texas streams. For permitting, instream flows are 40 percent of the median monthly flows from October to February; and 60 percent of the monthly median flows from March to September. The 60 percent values were chosen to provide more protection during the critical spring and summer months. The 40 and 60 percent levels were determined using the wetted perimeter relationship of the river, i.e., the amount of river bed and banks that are wetted from stream flow. At 60 percent of monthly median flow, more than 80 percent of the river substrate was wetted, but below 40 percent of the monthly median flow, the percentage of wetted substrate began to drop off significantly as portions of the stream bed were exposed due to the low water conditions (Figure 3-4). These threshold levels have been applied to most rivers in Texas to determine existing instream flows for water permitting. The second method that Texas uses to determine instream flows is the CCEFN, which is part of the Texas Guidelines for Regional Water Plan Development, produced by the Texas Water Development Board (TWDB, 2002b). These criteria are the result of collaboration among state agency scientists and engineers and local water resources representatives. CCEFN will be used in the second round of regional water planning in Texas, due to

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The Science of Instream Flows: A Review of the Texas Instream Flow Program FIGURE 3-4 Variation of wetted substrate with streamflow on the Guadalupe River below Canyon Reservoir. SOURCE: Data from Bounds and Lyons, 1979 be completed in 2007. All criteria are based on naturalized flows—the estimated flow that would have been present in a watercourse with no direct manmade impacts in the watershed. Criteria are defined in three zones for pass-through flows in reservoirs and for direct diversions from free-flowing streams and rivers (TWDB, 2002a). Whereas the Lyons method uses gage data as its flow value, CCEFN uses percentile values of the naturalized flow to determine direct diversion and pass-through flows. Unfortunately, this bifurcated approach to instream flow determination in Texas has created a system where the two methods produce different results for the same river (see Box 6-3 for further discussion). Flow Recommendations for the Savannah River The instream flow work in the Savannah River in Georgia and South Carolina began in 2002 and continues today. The U.S. Army Corps of Engineers (USACE) initiated a Comprehensive River Basin Plan to assess the degree to which various human needs and values for the Savannah were addressed through USACE water management, and whether changes in USACE dam operations might be warranted. With sponsorship from Georgia and South Carolina, the USACE worked with The Nature Conservancy (TNC) to facilitate a process for developing flow recommendations

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The Science of Instream Flows: A Review of the Texas Instream Flow Program to protect and restore the river, floodplain, and estuary ecosystems in the lower Savannah River. TNC organized an orientation meeting for stakeholders and interested parties. More than 60 scientists, water managers, and other representatives agreed on a one-year process to develop an initial flow recommendation that USACE could incorporate into its comprehensive plan for the river. The participants also identified specific scientists who should be involved in the process, as well as information sources thought to be useful in developing a flow recommendation. After the orientation meeting, the University of Georgia’s River Science and Policy Center produced a literature review and summary report (Meyer et al., 2003). The summary included statistical assessments of the available hydrologic data, a summary of the linkages between flow variations and the life cycles of numerous plants and animals, and a set of conceptual models of key hypotheses about flow-biota connections and human influences on key flow characteristics. These documents (Meyer et al., 2003) were circulated to more than 50 scientists identified during the orientation meeting who were invited to participate in a 3-day workshop to develop a flow recommendation for the Savannah River (Figure 3-5). Forty-seven scientists from more than 20 different state and federal agencies, academic institutions, and other entities participated in the flow recommendations workshop. During the workshop, they specified detailed flow requirements for a long list of target species and key ecosystem processes. The resulting flow recommendations differ among wet, average, and dry water years, and geographic location along the river. The Savannah River project is on-going, and it is too soon to determine the degree to which the flow recommendations have achieved the goals of the project. Still, the process of developing goals and deriving flow recommendations used in the Savannah River project shows how stakeholders and scientists can collaborate successfully on instream flow studies. For river basins that seek strong stakeholder involvement in an instream flow project, the Savannah River project is a working example of how stakeholders advance the process. Instream Flow Study of the Lower Colorado Basin The instream flow study of Mosier and Ray (1992) is a landmark study because it was the first comprehensive instream flow study carried out on a Texas river. The Mosier and Ray (1992) study is instructive to examine the way in which hydrology, biology, geomorphology, and water quality were

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The Science of Instream Flows: A Review of the Texas Instream Flow Program FIGURE 3-5 Flow recommendations for the Savannah River. NOTE: This is only one possible translation of the flow recommendations. For each water year type, a number of high flow pulses of varying magnitudes is specified to occur within a particular time window. drawn together to provide instream flow recommendations for the Colorado River below Austin, TX. The instream flow study was undertaken in response to a condition mandated in the 1988 adjudication of the Lower Colorado River Authority’s (LCRA) water rights in the river, and was carried out collaboratively by the LCRA and the TPWD. Upstream of Austin, the LCRA operates a sequence of six dams known as the Highland Lake reservoirs, and thus maintains significant control over flows in the lower river. From March to October, water is released from the Highland Lakes to supply water for rice irrigation along the Colorado River near the Gulf Coast. The release of irrigation supply water produces very large diurnal variations in discharge immediately downstream of Austin. During the winter months, irrigation water releases do not occur, and municipal wastewater discharges from the City of Austin are a significant part of the baseflow of the river immediately downstream of Austin. In making instream flow recommendations, Mosier and Ray (1992) defined four types of flows: Subsistence flow—the flow needed to maintain water quality conditions, especially dissolved oxygen levels, considered adequate to support the native aquatic community. Mosier and Ray made specific recom-

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The Science of Instream Flows: A Review of the Texas Instream Flow Program mendations for the Lower Colorado River using historical flow patterns and the QUAL-TX water quality model. Target flow—the flow regime that maximizes physical habitat complexity for the various components of the native aquatic community (see Figure 3-6). Hydraulic habitat analysis results in a schedule of monthly flows designed to optimize community diversity under conditions of normal rainfall. Under drought conditions, Mosier and Ray (1992) recommend reducing the discharge below the target flow but not below the subsistence flow. Critical flow—the flow distribution over time needed to support critical life history stages of certain components of the community, such as spawning and survival of fry. Maintenance flow—the flow conditions needed to scour the channel and prevent excessive siltation and macrophyte growth. Mosier and Ray (1992) offered the general recommendation that such flow pulses re needed but did not recommend a specific regime for them. The study of Mosier and Ray (1992) was mainly focused on how the patterns of releases from the Highland Lake reservoir system could be optimized to support aquatic life in the downstream river. Its results were used as part of LCRA’s Comprehensive Water Management Plan and resulting adjustments to its water permits for operating the Highland Lakes a were made by the Texas Natural Resources Conservation Commission (now TCEQ). Many of the rivers included in the proposed instream flow studies (lower Sabine, Trinity, Brazos and Guadalupe) all have large upstream reservoir systems whose releases affect their flows in an analogous manner to the lower Colorado River. The instream flow study of Mosier and Ray (1992) is a valuable guide as to how similar studies could be undertaken in those rivers. RESEARCH NEEDS FOR INSTREAM FLOW SCIENCE Instream flow science continues to evolve in its philosophy and application. Research is critical to its evolution. Instream flow research has gained momentum over recent years, particularly in areas that focus on technical disciplines of aquatic biology, hydraulics, hydrology, and geomorphology, and emerging technologies for sampling the river environment. Multi-disciplinary instream flow studies that combine two or more of these fields are also more common (see the International Symposia on Ecohy-

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The Science of Instream Flows: A Review of the Texas Instream Flow Program FIGURE 3-6 Habitat availability relative to a value of 1.0 at the target flow for the Colorado River at Bastrop. SOURCE: Mosier and Ray, 1992. NOTE: Figure depicts three relative habitat curves, for rapids, deep riffles, and shallow pools, and the mean relative habitat curve formed by averaging over 10 habitat types, rather than the three depicted. draulics2). With these advancements, major research needs and uncertainties still exist in the science of instream flows, especially with respect to integration, ecological indicators, and spatial scale. In instream flow science, integration combines the different technical components into one recommendation or a set of flow recommendations. Integration is an important, complicated step in the instream flow process. Integration methods are being developed empirically. Anecdotal accounts indicate that instream flow integration has been done several ways, such as having scientists make the decisions, involving stakeholders in the process, using quantitative models, and combinations of all three. These different approaches have not been researched in terms of cost, timeliness, applicability, or accuracy. No conventional methods define the state-of-the-science for how integration is done and no evaluation of current options exists in the peer-reviewed literature. Furthermore, methods used to integrate results from disparate studies into a flow recommendation have not been well documented. In order for the state of instream flow science to advance in this area, integration methods will need to be established, re 2   Further information on the most recent International Symposium on Ecohydraulics can be found online at http://www.tilesa.es/ecohydraulics/english/presenta.html.

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The Science of Instream Flows: A Review of the Texas Instream Flow Program viewed, and refined. Therefore, more information, research, and documentation are needed about the process of reaching final flow recommendations to strengthen instream flow science. Indicators are measurable quantities or variables that can be used to determine the degree that flow recommendations achieve the goals of the instream flow study or program. Indicators are important role in long-term instream flow monitoring and adaptive management. Ultimately, indicators guide informed policy decisions (NRC, 2000). Benefits of measurable indicators have been documented (GAO, 2004; NRC, 2000), along with the challenges associated with realizing those benefits, such as ensuring a sound indicator development process, obtaining sufficient data for reporting, co-ordinating data from multiple sources, and linking indicators to management programs and activities (GAO, 2004). Additional research is needed to develop criteria for ecological indicators (NRC, 2000) for use in instream flow studies. The physical, chemical, and biological processes of a stream ecosystem operate at different spatial scales and are expressed in different spatial dimensions over daily, seasonal, annual, and longer time periods (TPWD, TCEQ, and TWDB, 2003; Ward, 1989). Instream flow requirements must accommodate these processes at their respective, multiple scales. Determining appropriate scale(s) for instream flow work is challenging because the scale(s) must be fine enough to conduct field sampling and coarse enough to apply to larger regions and be efficient in use of resources. The success of integration methods and ecological indicators is very closely linked to spatial scale in instream flow work. For example, integrating disparate study results from biology and geomorphology technical evaluations will be more effective if the separate studies are conducted at similar or comparable spatial scales. A single set of ecological indicators (specific to river basins) needs to be selected carefully to ensure right process or function at the right spatial scale. The difficulty, therefore, is determining the appropriate spatial scale for instream flow study design, selection of models and tools, and integration of study results (TPWD, TCEQ, and TWDB, 2003). Spatial and temporal scaling issues remain an important, viable research area for instream flow science. SUMMARY Instream flow is a simple concept with the difficult task of balancing competing uses for river water. Over the three decades of instream flow work in the United States, four trends have marked its evolution:

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The Science of Instream Flows: A Review of the Texas Instream Flow Program from single, minimal flows to flow regimes; from a single-species focus to a focus on whole ecosystems; from the study of the stream channel to the study of riparian and floodplain areas, as well; and from a hydrology dominated field to an interdisciplinary field that includes hydrologists, biologists, lawyers, geomorphologists and water quality experts. State-of-the-art instream flow programs will strive to preserve whole ecosystems, mimic natural flow regimes, include riparian and floodplain systems in addition to the stream channel, take an interdisciplinary approach, use a variety of tools and approaches in technical evaluations, practice adaptive management, and involve stakeholders. Instream flow programs will encompass technical evaluations in biology, hydrology and hydraulics, physical processes, water quality, connectivity, and non-technical aspects of stakeholder involvement and goal setting. Integrating technical evaluations into a flow recommendation is an important, challenging task with few well documented methods. Three examples of current or recent instream flow work are highlighted that use a number of these components and show how instream flow studies and programs work in Texas and across the country. Still, there are some major research needs and uncertainties in the science of instream flows, especially with respect to integration, ecological indicators, and spatial scale.