5
Evaluation of the Texas Instream Flow Technical Overview Document

The Technical Overview Document (TOD; TPWD, TCEQ, and TWDB, 2003) outlines the methodological aspects of conducting instream flow studies in Texas rivers. The act of drafting this document is acknowledged as formidable because it must simultaneously provide (1) methods that are specific enough to guide technical evaluations, and (2) guidance that is broad enough to be applicable in individual subbasins across the different river systems in Texas. The Texas agencies faced a dilemma in writing the TOD because uniform approaches towards technical methods will be of little value to Texas with its wide range of riverine conditions, but the TOD cannot possibly make methodological prescriptions for every river system in the state. Therefore, the difficult task of preparing the TOD involves finding middle ground between these two options.

This chapter reviews and comments on the technical sections of the TOD and provides recommendations for its improvement. The TOD was evaluated for technical accuracy in the context of the instream flow program. The review of the TOD begins with a brief summary and description of the document’ s contents. Subsequently, a section on the overall findings of the TOD is presented, followed by individual evaluations of the subsections of hydrology and hydraulics; biology; physical processes; water quality; and integration and interpretation in the order they are presented in the original TOD. Implementation aspects are discussed in Chapter 6.

OVERVIEW OF TOD CONTENT

The TOD describes the methods to be used to collect, analyze, and integrate technical information among hydrologic, biologic, physical processes, and water quality aspects of instream flow study. The TOD is a fairly detailed document (74 pages) with more than 2,000 pages of supplemental, highly detailed, technical appendices. The appendices contain information mostly about the water quality programs in Texas, although other topics are



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The Science of Instream Flows: A Review of the Texas Instream Flow Program 5 Evaluation of the Texas Instream Flow Technical Overview Document The Technical Overview Document (TOD; TPWD, TCEQ, and TWDB, 2003) outlines the methodological aspects of conducting instream flow studies in Texas rivers. The act of drafting this document is acknowledged as formidable because it must simultaneously provide (1) methods that are specific enough to guide technical evaluations, and (2) guidance that is broad enough to be applicable in individual subbasins across the different river systems in Texas. The Texas agencies faced a dilemma in writing the TOD because uniform approaches towards technical methods will be of little value to Texas with its wide range of riverine conditions, but the TOD cannot possibly make methodological prescriptions for every river system in the state. Therefore, the difficult task of preparing the TOD involves finding middle ground between these two options. This chapter reviews and comments on the technical sections of the TOD and provides recommendations for its improvement. The TOD was evaluated for technical accuracy in the context of the instream flow program. The review of the TOD begins with a brief summary and description of the document’ s contents. Subsequently, a section on the overall findings of the TOD is presented, followed by individual evaluations of the subsections of hydrology and hydraulics; biology; physical processes; water quality; and integration and interpretation in the order they are presented in the original TOD. Implementation aspects are discussed in Chapter 6. OVERVIEW OF TOD CONTENT The TOD describes the methods to be used to collect, analyze, and integrate technical information among hydrologic, biologic, physical processes, and water quality aspects of instream flow study. The TOD is a fairly detailed document (74 pages) with more than 2,000 pages of supplemental, highly detailed, technical appendices. The appendices contain information mostly about the water quality programs in Texas, although other topics are

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The Science of Instream Flows: A Review of the Texas Instream Flow Program also covered. Appendices, background, and introductory material aside, the TOD has 8 major sections that correspond to the flowchart in the Programmatic Work Plan (PWP; see Figure 4-1): (1) study design; technical evaluations for (2) hydrology and hydraulics, (3) biology, (4) physical processes, and (5) water quality; (6) integration and interpretation; (7) study report production; and (8) monitoring and validation. Introduction and Ecological Setting The TOD opens with two sections, the Introduction and Ecological Setting, that present important background material that introduces the motivation of the Texas instream flow program and necessary components of an instream flow study. In the context of the state mandate to maintain a “sound ecological environment,” the ecological setting of rivers is described. Biology, hydrology and hydraulics, geomorphology, water quality, and connectivity are defined and introduced as the components of an instream flow study. Study Design Study Design (Section 3) is a short section that identifies the major steps necessary to begin an instream flow study. Basic steps for starting an instream flow study include compiling and evaluating existing information; identifying stakeholders; identifying appropriate study areas; conducting field reconnaissance, or initial technical assessments; preliminary biological and physical surveys; and the development of geographically-specific objectives and study plans. Without much detail, this section lays out the general approach to design an instream flow study in Texas. Hydrology and Hydraulics By far, the Hydrology and Hydraulics section (Section 4) is the most detailed section of the TOD. In it, technical aspects of hydrologic evaluation are discussed, such as historical, naturalized, and environmental flows and flow duration curves. Examples of types of hydrologic models are mentioned. Aspects of hydraulic modeling relevant to instream flow study are major segments, too, including some guidance on how to select a representative reach and methods for data collection. One- and multiple-dimensional modeling options are detailed. Large woody debris is consid-

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The Science of Instream Flows: A Review of the Texas Instream Flow Program ered a special challenge in hydraulics, and is discussed separately in this section. Biology The Biology section of the TOD (Section 5) outlines with specific methods for conducting baseline surveys and understanding instream habitat. Methods for surveys of instream habitat, fish, riparian systems, and macroinvertebrates are discussed in moderate detail. The TOD Biology section describes how to sample assemblages and measure habitat conditions, calculate habitat suitability criteria, integrate calculations with simulations of aquatic physical habitat, and integrate these calculations with simulated patterns of physical habitat dynamics. Instream and riparian habitat heterogeneity are also discussed in this section. Physical Processes Physical processes in the TOD (Section 6) refer to hydrogeomorphic riverine processes. Compared to the previous sections, physical processes is notably brief. This section of the TOD presents compact discussions of river classification, assessment of the current status of a river in terms of its geomorphology, and sediment transport processes. Flushing flows and valley, riparian, and channel maintenance physical processes are explained. For this section, the TOD focuses primarily on describing these processes, and only scantly mentions some general methods that can be employed to assess and measure physical processes in an instream flow study. Water Quality Water quality is unlike the other technical aspects of instream flow study in Texas because it is regulated at the federal and state levels. There are several well established water quality programs in Texas. The TOD section on water quality (Section 7) describes the state programs and provides relevant background and administrative history of these programs. The section on water quality for instream flow studies (Section 7.3) notes that applying water quality models used in the total maximum daily load (TMDL) and Texas Pollutant Discharge Elimination System (TPDES) programs to the instream flow studies will provide consistency among state programs. Water quality models for instream flow studies, according to

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The Science of Instream Flows: A Review of the Texas Instream Flow Program Section 7.3, should take into account spatial and temporal scales; geomorphic and hydraulic conditions of the water body; and the constituents of concern. Sampling or modeling methods for instream flow studies are not presented in the TOD section on water quality. Integration and Interpretation Findings from the technical evaluations (i.e., biology, physical processes, hydrology and hydraulics, and water quality) will be integrated to develop a flow recommendation. The integration section of the TOD (Section 8) describes the integration process in a framework (Section 8.1; see Figure 5-1) described simply as “the steps needed to develop flow regimes.” It also specifies that a quantitative analysis will be performed to identify critical relationships among the various technical aspects of an instream flow study. Instream habitat is defined as the integration of biology and hydraulics (Section 8.3) and will be predicted using a geographical information system (GIS)-based physical habitat model. The TOD presents ways in which such a model can be used. Habitat time series and habitat duration curves are described as tools for determining flow recommendations (Austin and Wentzel, 2001). The TOD stresses that many combinations of these spatial and temporal analyses can be used to identify target flow regimes. This section very briefly mentions how hydrology, physical processes, and water quality also need to be integrated into a flow regime recommendation. Quantitative Analysis (Section 8.7) includes a combination of statistical, time series, and optimization analyses. The TOD acknowledges that the “precise formulation of the instream flow optimization exercise has yet to be defined or tested,” but presents examples and scenarios in which such analyses could be useful in an instream flow study. Finally, this section of the TOD briefly discusses implementation issues (Section 8.8), but does not mention how flow recommendations will be implemented administratively, scientifically, or in combination with existing Texas water statutes and regulations. Study Report and Monitoring and Validation The TOD ends with a very short section that states a study report (Section 9) will be produced and submitted for peer review and the final section, Monitoring and Validation (Section 10), that mentions the importance of monitoring the effectiveness of the implemented flow regime(s). The

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The Science of Instream Flows: A Review of the Texas Instream Flow Program FIGURE 5-1 TOD Integration of instream flow study elements. SOURCE: Adapted from the TOD (TPWD, TCEQ, and TWDB, 2003). Monitoring and Validation section refers to Texas Commission on Environmental Quality’ s (TCEQ) surface water quality monitoring procedures and lists elements deemed important for a comprehensive monitoring program. STRENGTHS OF AND OPPORTUNITIES TO IMPROVE THE TOD The TOD sets out to prescribe the technical aspects, including methodologies, for conducting the detailed technical evaluations in the Texas instream flow program. This is a difficult charge to meet in a single document that is intended for diverse river subbasins across a large state. The TOD is evaluated in the following sections. The overall strengths of the document are listed first, some overarching opportunities to improve the TOD are presented next, and, finally, opportunities to improve the individual technical sections of hydrology and hydraulics; physical processes; biology; water quality; and integration and interpretation are discussed.

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The Science of Instream Flows: A Review of the Texas Instream Flow Program Strengths of the TOD The Texas agencies are commended for drafting a document that has several strengths. The main strength of the TOD is that it encompasses the primary elements of separate technical evaluations relevant to a larger instream flow study. Technical areas of hydrology and hydraulics, physical processes, biology, water quality and connectivity are recognized as important elements and described in the TOD. The TOD also includes initial approaches for integrating results into a flow recommendation. It cannot be overstated how complicated inter-disciplinary instream flow studies can be, and Texas has made a commendable effort in designing its instream flow program to be comprehensive. The biology and hydrology and hydraulics sections reflect a commanding understanding of the relevant issues for instream flow work in Texas rivers. Finally, the TOD represents cooperation among three state agencies with separate missions. Presentations in the TOD reveal the relative expertise of each agency and hint at the promise of these three agencies working together successfully to design and implement a benchmark instream flow program in Texas. Overarching Opportunities to Improve the TOD The TOD is composed of several individual pieces that comprise the technical aspects of the Texas instream flow program. The TOD presents each technical piece and the process by which the pieces will be integrated (Figure 5-1) into a flow recommendation. The sharp focus of the TOD is on the distinct, technical pieces of the instream flow study; however the real challenge in instream flow science, and the weakness of the TOD, is the connections among these pieces. Landscape ecology metrics and connectivity can help strengthen these connections. Chapter 3 outlines seven principles of a state-of-the-art program. The top three principles are to (1) preserve whole functioning ecosystems; (2) mimic, to the extent possible, a natural flow regime; and (3) expand the spatial scope of instream flow studies beyond the river channel to include the riparian corridor and floodplain systems. The whole ecosystems, natural flow regime, and the expanded spatial scale can be viewed as landscape ecology metrics of instream flow science. Used as the focus of the technical evaluations, these metrics can guide the development of instream flow recommendations. Methods by which landscape ecology elements guide an instream flow study are also listed in Chapter 3 as the last four principles: conducting studies using an interdisciplinary approach; using a variety of tools and approaches tailored to the subbasin characteristics; using adaptive

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The Science of Instream Flows: A Review of the Texas Instream Flow Program management; and involving stakeholders in the process. Together, these seven principles, viewed as landscape metrics and methods, can be used to set instream flow requirements in a state-of-the-art instream flow program. Connectivity is defined in the TOD as the “movement and exchange of water, nutrients, sediments, organic matter, and organisms within the riverine ecosystem” (TPWD, TCEQ, and TWDB, 2003). It is discussed in two paragraphs in Section 2, Ecological Setting, but not in the subsequent technical evaluation sections of the TOD. Whereas the TOD defines the concept of connectivity well, it never addresses how connectivity is a part of the Texas instream flow program. The brief, early section on connectivity lays out a nice structure in which technical evaluations could be designed or integrated; unfortunately, connectivity is not revisited in subsequent sections of the TOD. Connectivity reflects important aspects of instream flow science and the TOD should address how connectivity will be used in the detailed technical evaluations. The dimensions of connectivity occur laterally, longitudinally, vertically, and temporally. These dimensions could be used as organizing axes for developing the conceptual models (see Table 3-2) and designing technical evaluations. Connectivity dimensions also can be used to calibrate the spatial scale of the technical evaluations to ensure compatibility and smooth integration of results. For example, the lateral dimension across a stream channel and associated floodplains could establish the spatial scale for technical evaluations of sediment erosion and deposition, flooding frequency and magnitude, aquatic and riparian species, and variation in water quality. Reconnaissance data could be collected on these assays and entered into a matrix (i.e., Table 3-2) to create a conceptual model that informs the detailed technical evaluations. Three other overarching findings come from evaluating the TOD. First, for each technical evaluation (i.e., hydrology/hydraulics, physical processes, biology, and water quality), the TOD makes little distinction among individual basins and presents one or a very few approaches that may not be appropriate in all basins and subbasins. Of course, the TOD cannot possibly list all approaches for all possible scenarios in Texas rivers, but it should identify that a range of models, approaches, and tools may be necessary to address the highly variable characteristics of each study subbasin. Second, considerable inconsistency is found in the level of detail among the technical sections. Some sections have highly detailed methodological processes (hydrology and hydraulics, biologic sampling), but other sections outline only very general sampling methods or none at all (integration, physical processes, and long term monitoring and validation).

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The Science of Instream Flows: A Review of the Texas Instream Flow Program Finally, many of the methods presented in the TOD lack context because measurable instream flow goals are not clearly articulated. It is under-standable that the goals for the individual basin studies will vary from basin to basin and all goals cannot be identified in the TOD. Still, the TOD very briefly mentions goals (i.e., biological diversity and biological integrity) and does not discuss the methods in the context of a state-wide program or goals. Without a clearly defined goal statement or process to identify it in the PWP or TOD, the context for these technical studies is unclear. Hydrology and Hydraulics Overall, the section on hydrology and hydraulics demonstrates a solid understanding of the state-of-the-art in hydrologic and hydraulic methods used in the scientific and engineering community. Compared to other chapters in the TOD, Section 4 (Hydrology and Hydraulics) is quite specific about what tasks will be performed and the tools that will be used. The Texas agencies are commended for the high level of sophistication and detail presented in the hydrologic/hydraulic section of the TOD. The weakness with the hydrologic/hydraulic TOD material is that the detailed and sophisticated methods presuppose that all techniques are applicable in all Texas basins. The hydrologic/hydraulic TOD section describes specific approaches that may not be necessary in or appropriate for all instream flow studies. A better approach to hydrology and hydraulics is to outline specific methods that could be applied in different circumstances to assure a consistent approach across the state that has enough flexibility to accommodate the variety of river systems within Texas. This improved approach will strengthen the study design phase and reduce the cost of hydrologic/hydraulic sampling and modeling by eliminating unnecessary analyses. Furthermore, connections are not explicit between the hydrologic/hydraulic techniques presented and a sound ecological environment, instream flow study goals, or the other technical disciplines of instream flow study, such as biology or water quality. The purpose of hydraulic modeling is to define the streamflow characteristics (e.g., depths and velocities) as a function of discharge. As presented in the TOD, results from hydraulic modeling subsequently will be used to assess biological, water quality and physical processes in instream flow systems. The problem in the TOD is that these models and the results from these models are related loosely, if at all, to the other technical elements and studies. It is unclear in the TOD whether the spatial scale of the hydrologic/hydraulic studies coincides with the spatial scales of the biology, physical processes, or water quality empirical studies. A stronger connec-

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The Science of Instream Flows: A Review of the Texas Instream Flow Program tion among “the master variable,” hydrology, and the other instream flow technical elements will be very important to ensure that the sophistication of the hydrologic/hydraulic tools, models, and methods is appropriate and efficient for achieving instream flow study goals. Therefore, the TOD should be revised to include explicit connections to the other technical studies to ensure that hydrologic/hydraulic technical assessments are relevant to achieving instream flow study goals, including a sound ecological environment. The TOD and the PWP mention how hydrology is affected by human uses in the watershed. Several of the supporting documents indicate the profound effect of reservoirs on Texas rivers. Reservoirs are important considerations in Texas, as all major rivers in Texas are dammed for hydropower, municipal, or irrigation purposes. One important element missing from the hydrologic/hydraulic TOD section is a method to relate reservoir operations to instream flows. For some distance below a dam, a river’s hydrology, water quality, substrate, and biota will be greatly affected by the dam’s operation. The TOD also does not discuss how instream flow characteristics may change due to watershed and land use changes, such as increases in urbanization, irrigation, and impervious surface area in the watershed. Water managers have many options to affect instream flows, including dam operation, as well as issuance of water permits to withdraw water from or discharge water to a river. The TOD needs revision to consider approaches for predicting instream flow levels that take into account reservoir operations, permitting, and other watershed land uses. Some of the two- and three-dimensional models presented in the TOD are highly sophisticated. These models require high quality input data to produce high quality, sensitive and very detailed output data about streamflow characteristics. The hydrologic/hydraulic models presented in the TOD appear too detailed for and therefore misaligned with, some of the other technical studies. For example, aquatic habitat in Texas is classified in the Aquatic Life Use scale as “Exceptional,” “High,” “Intermediate,” or “Limited.” The TOD suggests that results from hydraulic analyses can be used to broadly classify aquatic habitat in these categories. If aquatic habitat is classified in such qualitative terms, then highly quantitative outputs of hydraulic modeling may not be needed for such classification. Another example of misalignment is with spatial scale. The accuracy of two- and three-dimensional hydraulic models is dependent on the spatial density of the data. These time- and resource-intensive models require suitably accurate input data. Some biological or geomorphic empirical studies will take place over larger spatial areas, such as over the floodplain of a segment or the home range of a key fish species. In these cases, the limited spatial scale of a hydraulic model is too fine to be of use to the geomorphic

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The Science of Instream Flows: A Review of the Texas Instream Flow Program or biologic assessments. The methodologies presented in hydrology/hydraulics section of the TOD need better alignment with the other technical aspects of the instream flow studies in terms of model sophistication, sensitivity of model output, and spatial scale. The authors of TOD Section 4 clearly have a good understanding of hydraulics, methods for gathering hydraulic data, and one- and two-dimensional flow modeling. The remaining challenge is the development of quantitative relationships between hydraulics and specific elements of a sound ecological environment. Given that rather short duration streamflow phenomena can be critical for many aquatic and riparian biota, the TOD appropriately proposes to develop naturalized flow series using daily time steps by disaggregating naturalized monthly flows from the water availability models (WAM) used for water rights permitting in Texas. Nevertheless, the TOD needs revision to make stronger connections among the naturalized flow series and biologic or other aspects of instream flow. Summary: Hydrology and Hydraulics Hydrology is often referred to as the “master variable” in an instream flow context because all the other aspects relate to it. Biology, physical processes, and water quality aspects of instream flow work all can be tied to components of the hydrologic regime. Indeed, the TOD and PWP suggest strongly that the intention of the Texas program is to capitalize on these naturally occurring connections to develop a strong, comprehensive instream flow program for the state. Quantifying streamflow characteristics requires highly technical methods and models, and the hydrology/hydraulics section of the TOD reflects an impressive knowledge of such approaches. Despite its level of detail and sophistication, the hydrology/hydraulics section of the TOD needs significant revision to: Include explicit connections to the other technical studies to ensure that hydrologic/hydraulic technical assessments are relevant to achieving instream flow study goals, including a sound ecological environment Consider approaches for predicting instream flow levels that take into account reservoir operations, permitting, and other watershed land uses Align more closely with the other technical aspects of the instream flow studies in terms of model sophistication, sensitivity of model output, and spatial scale Make stronger connections among the naturalized flow series and biologic or other aspects of instream flow

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The Science of Instream Flows: A Review of the Texas Instream Flow Program Biology The general strengths of the Texas TOD section on biology include a strong introductory section that provides an excellent overview of the literature and major issues associated with choice of biological response variables and methods of data collection and analysis for instream flow recommendations. The TOD also provides an outstanding general discussion of the important issues of habitat scale, ecological processes, and species life histories. However, the TOD Biology section gives a limited description of the program’s rationale and plans for implementing alternative methods for field sampling, data analysis, and derivation of flow recommendations. The connection between the biological surveys and goals of the instream flow program or of individual studies is not discussed in this section. Program elements related to biology are discussed here in the order that they appear in the TOD. Baseline Information The TOD baseline information section correctly identifies the starting point for a biology survey that is part of an instream flow study. The TOD highlights steps to take at the beginning of a biology sampling effort: compiling existing information, soliciting stakeholder involvement, and inventorying the types of information that will likely be needed in the biological survey (i.e., life history traits, environmental requirements, species distribution, community composition, and connectivity considerations). The TOD sets forth four types of surveys, or field reconnaissance, to be done in the process of gathering baseline information: instream habitat, fish, macroinvertebrate, and riparian surveys. All except the riparian survey section are described at a decent level of detail; the riparian survey section is brief and lists only the types of information to be considered or collected. The field reconnaissance measures, as outlined, appear logical and sufficient, and the need for gathering and evaluating baseline information is well defended in the TOD. However, the TOD does not adequately illustrate the availability of specific data sources, the manner in which data will be gathered and analyzed, and how these analyses will influence the design and implementation of specific studies. The TOD states that “ecological integrity” will be assessed at the reach scale, but the specific metrics for estimating ecological integrity are not identified, with the exception of using the TCEQ standard protocol for determining the appropriate Aquatic Life Use designations of surface waters. The metric developed by Texas Natural Resources Conservation

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The Science of Instream Flows: A Review of the Texas Instream Flow Program TABLE 5-2 Aquatic Life Attributes for Aquatic Life Categories Aquatic Life Use Habitat Characteristics Species Assemblage Sensitive Species Diversity Species Richness Trophic Structure Exceptional Outstanding natural variability Exceptional or unusual Abundant Exceptionally high Exceptionally high Balanced High Highly diverse Usual association of regionally expected species Present High High Balanced to slightly imbalanced Intermediate Moderately diverse Some expected species Very low in abundance Moderate Moderate Moderately imbalanced Limited Uniform Most regionally expected species absent Absent Low Low Severely imbalanced   SOURCE: TNRCC, 2000.

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The Science of Instream Flows: A Review of the Texas Instream Flow Program The Texas TMDL Program The TMDL program in Texas1 is the primary mechanism to remedy impairments to water quality. A TMDL is “the total amount of a pollutant a water body can assimilate and still meet state water quality standards” (TNRCC, 1999). TMDL development has come to prominence in recent years because many water bodies are not “swimmable and fishable,” despite significant water quality improvements due to controls on end-of-pipe wastewater discharges. TMDLs include point- and non-point sources, such as pollution from watershed runoff, atmospheric deposition, and contaminated sediments. The Texas TMDL program relies on water quality models that estimate nutrient, bacterial, and other pollutants in surface waters. QUAL-TX and seven other models are currently used in TMDL studies in Texas. The applicability of these models in an instream flow context, however, is untested. Of the models used in the TMDL program (QUAL-TX; Mass Balance or CSTR; HSPF; WASP; QUAL2E; SWAT; EPIC; and EFDC), QUAL-TX has been relied upon most heavily and is therefore the focus of this discussion. QUAL-TX is a modification to the federal QUAL2E2 model. It has been tailored for Texas river conditions, such as a site specific equation for stream reaeration. QUAL-TX is a steady state model for which the discharge is set at a small value, such as the 7 day 2 year low flow. It is most often used to estimate effects of wastewater discharge on dissolved oxygen (DO) during very low flow conditions. In some river basins, such as the San Antonio Basin, the TCEQ has developed and maintained a suite of QUAL-TX models for segments of the San Antonio River and its principal tributaries to help assess wastewater discharge permit applications. QUAL-TX is a mainstay of the Texas wastewater discharge permitting process, and it has also been applied in about one third of the TMDL studies undertaken to date by the agency (Table 5-3). However, this model has several limitations when considering instream flow specification. Principal among them is that the model is a static or steady state model, which means 1   For further information on the Texas TMDL program see the TNRCC website at http://www.tnrcc.state.tx.us/water/quality/tmdl/index.html. 2   The QUAL model was originally developed in Texas and later further developed and adopted for national use by EPA.

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The Science of Instream Flows: A Review of the Texas Instream Flow Program TABLE 5-3 Use of Water Quality Models in TMDL Studies in Texas Model Number of TMDL studies QUAL-TX 9 Mass Balance or CSTR 4 HSPF 3 WASP 3 QUAL2E 2 SWAT 2 EPIC 1 EFDC 1 No model used 5 Total 30   SOURCE: Data from G. Rothe, TCEQ, personal communication, 2004. it operates only for a single streamflow discharge, but an instream flow assessment has to consider a whole range of flows that may occur and their time patterns of occurrence. QUAL-TX operates on river or stream segments ¼ mile to 1 mile long. The model yields an average dissolved oxygen value for a river reach that contains many mesohabitat zones and associated aquatic communities. QUAL-TX also accounts for spatial variations in water quality between water in the center of a stream and that along the banks, and the vertical variations in dissolved oxygen content with depth. Another limitation of QUAL-TX is that it assumes a flat-bed stream, i.e., the bottom area of the stream does not change as the flow approaches zero. A real stream has spatially varying bed topography; therefore higher areas of the stream bed are exposed and become dry as flow diminishes, and lower parts remain submerged longer than would be if the bed were flat. Although some of the other water quality models are dynamic and offer a greater range of possible bed geometries than QUAL-TX, the other models used in the TMDL program still employ spatial computational units of the same order of size as QUAL-TX. It might be possible through field scale research to quantify the spatial and temporal variations of dissolved oxygen within a reach so that with a daily and reach-averaged dissolved oxygen concentration available, some type of “down scaling” process could be applied to infer the spatial and temporal patterns of dissolved oxygen at the meso- and microhabitat scale. In the four part instream flow regime (subsistence flows, base flow, high pulse flows, and overbank flows) (see Figure 3-2, Table 3-2), QUALTX may be useful in establishing the subsistence flow. In other words, QUAL-TX could estimate the flow needed to maintain minimum water quality standards. Since depressed DO impairs Aquatic Life Use in many streams in Texas, QUAL-TX may be a useful means of examining what

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The Science of Instream Flows: A Review of the Texas Instream Flow Program flows are needed to maintain adequate levels of dissolve oxygen during low flow conditions. However, the water quality component of an instream flow technical evaluation should involve other aspects, as well, including suspended sediment, temperature, and other water borne nutrients and pollutants. The flow regime and the various constituents of water quality act together to produce a sound ecological environment and these aspects need to be considered when defining instream flow requirements for a particular river. Ideally, a water quality and temperature simulation model for instream flow assessment needs would allow for: Time varying hydrology across the full range of flow variation from floods to drought low flows The effect of management variations such as alternative strategies for releasing water from reservoirs watershed processes for sediment production and nonpoint source pollution generation point sources of pollution from wastewater discharges instream processes of chemical transformation and sediment transport local scale variations in flow and water quality characteristics within stream mesohabitats and microhabitats There is no single simulation model currently available which can perform all of these functions. A mechanism is needed to combine hydrologic, water quality and hydrodynamic models across spatial scales to achieve this range of capabilities. The emerging technology of Hydrologic Information Systems is providing some capabilities that could contribute to this goal (Maidment, 2002). Summary: Water Quality While just as important as hydrology and hydraulics, biology, and physical processes in a Texas instream flow program, water quality is treated differently than its sibling components. Water quality is a regulated entity in Texas and has a well established set of state and federal programs. The TOD ably describes these programs. These programs, administered by TCEQ, meet their purposes of ensuring that surface waters in Texas comply with regulatory standards. Instream flow considerations are not the focus of the state’s water quality programs. Therefore, the instream flow

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The Science of Instream Flows: A Review of the Texas Instream Flow Program program’s elements that contend with water quality must be aligned with the existing water quality programs, so as to avoid conflicting requirements for maintaining sound ecological environments in Texas rivers. The TOD presents more than 2,000 pages of water quality material. A significant limitation of the TOD water quality section is that it does not refer to this material or discuss how the water quality component of an instream flow assessment should be conducted, or how instream flow and water quality considerations can be integrated with each other. The Texas TMDL program’s aim is to improve water quality in Texas surface waters. In total, eight water quality models are used in the TMDL program, with QUAL-TX used more than the seven others. QUAL-TX is a steady state model that models DO. QUAL-TX is applicable to instream flow studies in that (1) DO is an important constituent of water quality that strongly influences aquatic biology; (2) QUAL-TX has an established record of use in Texas, including use with Aquatic Life Use designations; and (3) it operates on the same spatial scale as many biological sampling efforts. The primary limitations of the model include (1) it models DO for only one discharge at a time and instream flow studies require water quality measurements over a range of flows; and (2) DO is only one constituent of water quality, when others, such as suspended sediment, also influence a sound ecological environment. The eight models used in the TMDL program can address discrete pieces of water quality as it relates to instream flow studies, but none can simulate all of the aspects that need to be included in a comprehensive instream flow technical evaluation. The water quality component of the Texas instream flow program reflects the existing strengths of the Texas water quality management program. These strengths include a comprehensive water quality database for Texas streams and rivers, an established set of water quality standards, and procedures for assessing compliance with them, including standards for aquatic life. The TOD does not define how these existing procedures will need to be adapted or refined for use in an instream flow assessment. A significant limitation of the bioassessment component of the existing water quality program is the lack of a comprehensive database of empirical biological information compared to extent and history of the data maintained by the TCEQ on water quality. The major findings and recommendations for the water quality component of the TOD are: The TOD, with appendices, presents thorough documentation of the Texas water quality programs, but does not outline how this program can be integrated with or used in an instream flow program.

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The Science of Instream Flows: A Review of the Texas Instream Flow Program QUAL-TX is a steady state model that can accurately model DO for a single rate of flow, a limitation for a comprehensive instream flow technical evaluation. However, there is no single simulation model currently available which can model all instream flow functions, and a mechanism is needed to combine hydrologic, water quality and hydrodynamic models across spatial scales. A more comprehensive method is needed for storing all the biological and physical data acquired during Aquatic Life Use assessments, and a more complete digital inventory of biological data on the past condition of Texas streams and rivers needs to be compiled. The instream flow program should be integrated with water quality, water permitting and other water-related programs in Texas to avoid conflict or establish support between the water quality and instream flow programs. Integration and Interpretation Integration of the results of the hydrology, biology, water quality and physical process investigations into flow recommendations is critical to the success of any instream flow study. This is a very difficult task because the methods for integration are not well documented (see Chapter 3), and too often, the individual investigations are not designed to be integrated with each other. The Integration and Interpretation section of the TOD (Section 8) presents a process (Figure 5-1) to derive a flow recommendation that uses instream habitat models to integrate hydraulics and biology. The Integration section of the TOD has an in-depth review of quantitative analyses and a very brief section about hydrology, water quality, and physical processes integration. The TOD describes a vague integration process that is based on several assumptions. It is assumed that relevant aspects of aquatic habitat can be modeled by habitat models. It is also assumed that a standard set of techniques and models will be applied in all river basins. The TOD states that integration is to be accomplished mainly through quantitative analyses, but these analyses are not described in enough detail or in context to guide consistent, repeatable studies in river basins across the state. These assumptions need to be better explained and defended in the TOD to provide much needed support for the integration process presented. The main weaknesses of the integration section are that (1) it is represented by a complicated Integration Framework (Figure 5-1) that is never thoroughly explained; (2) it does not mention the goals of the study as part

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The Science of Instream Flows: A Review of the Texas Instream Flow Program of the integration process; (3) the process of how technical evaluations (Sections 4, 5, 6, and 7) are used to derive flow recommendation is not well described; and (4) the integration of biology and hydraulics is given far more attention than the other technical aspects of water quality, physical processes, and hydrology. While the purpose of integration is to pull all of the elements together, this section of the TOD ultimately stands alone. With few exceptions, the material in this section makes no reference to the technical evaluations of the previous sections of the TOD, and the previous TOD sections do not mention that results from sampling efforts will ultimately be used in the Integration Framework. That said, the integration phase of any instream flow study is decidedly the most difficult, and methods to integrate several interdisciplinary studies into a single flow recommendation are not well documented in the current literature (IFC, 2002; Postel and Richter, 2003). Examples of possible approaches to Integration are the Building Block or Percent-of-Flow (Flannery et al., 2002) approach (see Chapter 3). The Building Block approach essentially builds a recommended instream flow hydrograph, or set of hydrographs, using key pieces of information developed during technical studies. The percent-of-flow approach uses results from the technical evaluation to determine appropriate levels of allowable flow depletion (typically expressed as percentages of the natural flow) during different times of the year, or during different water year types. These are just two approaches to integrating the various aspects of instream flow studies. Other approaches are being used and developed, but very few are well documented. Integration should be conceived early in the study design phase to ensure that studies fit together conceptually and are aligned with each other and program and subbasin goals. This type of integration between disciplines may require different models than those models routinely used within disciplines, different sampling methodologies, or sampling at different spatial scales. In these and maybe other ways, the state agencies may have to adopt new approaches to data collection and analyses, since the agencies normal intra-disciplinary practices may not lead to an integrated approach. The Framework Arguably, the Integration Framework (Figure 5-1) which is intended to illustrate “the steps needed to develop flow regimes” is the most critical element of the TOD’s integration process. However, the framework in the TOD is presented very briefly in one short paragraph; the framework figure does not indicate any order of sequence; and the boxes of the framework

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The Science of Instream Flows: A Review of the Texas Instream Flow Program contain general topics, not “steps,” towards integrating across several disciplines and technical evaluations. The Integration Framework is very difficult to navigate. Furthermore, the framework figure omits program or study goals, without which, the purpose of and connections among the integration efforts and goals is obscure. In order to be useful, the Integration Framework must be described more thoroughly in the text and/ or revised to articulate the specific steps to be taken or specific points of consideration in the process of developing an instream flow recommendation. Instream Habitat The Instream Habitat sub-section (Section 8.2) describes how GIS-based physical habitat models, hydraulic models, and habitat time series can be used to integrate hydraulics and biology for instream flow purposes. The TOD presents these models as a menu of options that can be used separately or in combination to identify flow regimes in all river basins, but it does not give guidance as to under which circumstances each model is most appropriate. The models are adequately described in terms of what function each model fulfills; however their position(s) in the flowchart and methods used to derive a flow recommendation are not explained. This section states that instream habitat models will be used with output from the hydraulic and biological technical evaluations, but the earlier technical sections of the TOD do not indicate that their results or output will be compatible with these instream habitat models. The instream habitat models focus exclusively on integrating hydraulics with biology, and leaves unclear whether any models can be used to integrate hydrology, water quality, and physical processes. Quantitative Analysis Aside from a passing reference to statistical and time series analyses, the section on quantitative analyses (Section 8.7) focuses almost exclusively on optimization analyses. Optimization analysis is proposed as a technique to “identify and evaluate alternative flow conditions that maximize, or at least preserve, ecological health” (TPWD, TCEQ, and TWDB, 2003). The goal of optimization is to make a “best” or optimal decision. Optimization has the benefits of being quantitative and leading to a single alternative; however optimization has significant shortcomings as a primary method for reaching an instream flow recommendation. A main shortcoming is that optimization is a mathematical function that cannot easily include broad

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The Science of Instream Flows: A Review of the Texas Instream Flow Program ecological, legislative or social goals in its syntax. Furthermore, the type of optimization presented in the TOD “has yet to be defined or tested.” Hydrology, Biology, Physical Processes, and Water Quality Sections These four sections, plus a fifth, Other Integration Considerations, are very brief recaps of the important elements that should be included in an integration exercise. These sections are too brief to be useful in guiding integration processes and need significant augmentation. Summary: Integration and Interpretation With little doubt, the integration phase is the most difficult and least documented phase in instream flow science. Most often, the purpose of this phase is to pull together results from different technical evaluations into a single flow recommendation, but the process could be more efficient if integration is conceived in the early study design phase and focuses on common goals or objectives. Various models (GIS-based physical habitat models, hydraulic models, habitat duration curves) and quantitative tools can be helpful to derive a flow recommendation, and some of those tools are introduced in this section. The Integration and Interpretation section of the TOD needs significant revision to: correspond more strongly to the methods presented in the biology, hydrology and hydraulics, water quality and physical processes sections of the TOD; revise the Integration Framework to include sequential steps and clearer direction of how to combine results from the technical evaluations with appropriate models to derive flow recommendations; and augment sections on integrating Hydrology (Section 8.3), Water Quality (Section 8.4), Physical Processes (Section 8.5) and Other Integration Considerations (Section 8.6) to equal in detail and application those presented in Instream Habitat (Section 8.2). SUMMARY AND RECOMMENDATIONS The TOD sets out methods for the technical evaluations of hydrology and hydraulics, biology, physical processes, and water quality in the Texas

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The Science of Instream Flows: A Review of the Texas Instream Flow Program instream flow program. The Texas TOD (1) makes little distinction among individual basins and sets forth a standardized set of tools for use in river basins that are highly variable across the state; (2) is inconsistent in the level of detail among the four technical sections; (3) encompasses the primary elements of separate evaluations relevant to a larger, instream flow study, those of hydrology and hydraulics, biology, physical processes and water quality, with tenuous connections among them and vague associations to an instream flow recommendation; and (4) presents methods that lack context because measurable instream flow goals are not clearly articulated. Therefore, the TOD is recommended to be revised to: strengthen linkages among individual studies on instream biology, hydrology and hydraulics, physical processes, and water quality, and stronger connections between studies and components of flow regime; include greater capacity for and reference to site-specificity at the (sub) basin-scale; design the biological, physical processes water quality, and hydrology and hydraulics instream flow studies at commensurate spatial and temporal scales to improve the ability to integrate findings from the various technical evaluations into a single flow recommendation; strengthen the physical processes section to align more closely with the hydrology and hydraulics and biology sections; clarify methods and the flowchart in the Integration and Interpretation section; describe how connectivity will be used in the Texas instream flow studies; augment the monitoring and validation (i.e., adaptive management) section to monitor progress towards meeting the stated goals; and establish means to set goals for the individual studies that relate to the state-wide definition of a sound ecological environment. In general, the major findings and recommendations for each technical section are as follows: Hydrologic and hydraulic technical studies reflect a significant understanding of hydrology, hydrologic measurements, and analyses commonly required for performing instream flow studies. The TOD presents highly sophisticated yet standardized hydrologic and hydraulic analyses. Not all models, however, will fit all streams and the analytical approaches should be more closely tailored to the specific objectives of the instream flow study.

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The Science of Instream Flows: A Review of the Texas Instream Flow Program The physical processes section is notably brief, especially in comparison to the hydrology and hydraulics and biology sections. It omits discussions about Texas hydrologic regimes as they relate to physical processes, GIS applications, sediment budget estimates, and impacts of changes in land use, population, and climate in the watershed over time. The physical processes section needs to be expanded to be comparable to the hydrology and biology sections and include discussions on Texas hydrologic regime, GIS application, sediment budget analyses, and impacts of land use, populations and climate changes in the watershed. Texas regionalized IBIs should be evaluated for application to instream flow studies and larger rivers; these evaluations should be published in the open, peer-reviewed scientific literature as a means to validate the Texas approach. The instream flow program should be integrated with water quality, water permitting and other water-related programs in Texas to avoid conflict between the water quality and instream flow programs. The Integration Framework (TOD Figure 8.1) needs be revised to include sequential steps and clearer description of the proposed process to derive flow recommendations from combining results from the technical evaluations with appropriate models.