7
Conclusions and Recommendations

In the preceding chapters, the committee has explored in detail the Natural Flow Study (USBR 2005) and the Instream Flow Study (Hardy et al. 2006a) and assessed the scientific validity of the models produced by each study. Because the overall objective of the U.S. Bureau of Reclamation (USBR) has been to use the products of these studies to determine target flows for the Klamath River that can benefit coho and chinook salmon, the committee also evaluated the utility of the models and their outputs in potential support of regulation of river flows. In this chapter, the committee identifies the common threads that arose from its investigations and reviews the conclusions and recommendations that emerged from its assessments.

THE BIG PICTURE

The committee’s considerations of science and decision making in the Klamath River basin identified the same overarching concern at almost every turn. The committee found that science was being carried out piecemeal, sometimes addressing very important questions, but not linking them to other relevant questions and studies. The Natural Flow Study (USBR 2005) and the Instream Flow Study (Hardy et al. 2006a) were major science and engineering investigations, but the linkage of one to the other was only partially achieved. Other studies in the basin, such as the U.S. Geological Survey’s (USGS’s) hydrologic studies in the Sprague River basin and the extensive research in the Trinity River basin (both of which are part of the



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7 Conclusions and Recommendations In the preceding chapters, the committee has explored in detail the Natural Flow Study (USBR 2005) and the Instream Flow Study (Hardy et al. 2006a) and assessed the scientific validity of the models produced by each study. Because the overall objective of the U.S. Bureau of Reclamation (USBR) has been to use the products of these studies to determine target flows for the Klamath River that can benefit coho and chinook salmon, the committee also evaluated the utility of the models and their outputs in potential support of regulation of river flows. In this chapter, the committee identifies the common threads that arose from its investigations and reviews the conclusions and recommendations that emerged from its assessments. THE bIG pICTuRE The committee’s considerations of science and decision making in the Klamath River basin identified the same overarching concern at almost ev- ery turn. The committee found that science was being carried out piecemeal, sometimes addressing very important questions, but not linking them to other relevant questions and studies. The Natural Flow Study (USBR 2005) and the Instream Flow Study (Hardy et al. 2006a) were major science and engineering investigations, but the linkage of one to the other was only partially achieved. Other studies in the basin, such as the U.S. Geological Survey’s (USGS’s) hydrologic studies in the Sprague River basin and the extensive research in the Trinity River basin (both of which are part of the 211

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212 HYDROLOGY, ECOLOGY, AND FISHES OF THE KLAMATH RIVER BASIN Klamath River basin), seem not to have had any influence on each other or on the flow studies examined in this report. The committee found that important characteristics of research for management of a complex river basin were missing from Klamath River studies: the need for a “big picture” perspective based on a conceptual model encompassing the entire basin and its many components. As a result, the integration of individual studies into a coherent whole has not taken place, and it is unlikely to take place under the present conditions. It also is not clear how much influence previous reports that have argued for integration (for example, Braunworth et al. 2002, IMST 2003, NRC 2004a) have had. As shown in the previous chapters and summarized below, the commit- tee found shortcomings in the Natural Flow and Instream Flow studies that are sufficiently serious that the committee questions whether the studies can guide decision making effectively. To address science and management in the basin, the committee first recommends that the agencies, researchers, decision makers, and stakeholders together define basin-wide science needs and priorities. One method of achieving success in this effort would be through the establishment of an independent entity to develop an integrated vision of science needs. The body that defines this vision must be viewed by all parties as truly independent for it to be effective, unlike the Conser- vation Improvement Program, which, despite good intentions, appears to many people in the region as a creature of the USBR and is therefore to be associated with the Bureau’s official mandates and responsibilities. If the proposed task force reports to the secretary of the U.S. Department of the Interior (DOI), rather than to any specific agency, it is more likely to avoid the appearance of being controlled by any particular agency or interest group in the basin and thus is more likely to be and to appear independent. Leadership of the task force by a senior scientist who reports to the sec- retary would be a major step toward removing perceived biases in science and its application. The committee concludes that when the science needs for the Klamath River basin are better characterized, the individual studies necessary to create a sound, science-based body of knowledge for decision makers and managers will be more easily identified. Only if this general vision and process determines that the Natural Flow Study and the Instream Flow Study might help to satisfy science needs in the basin should investigators seek to address the shortcomings that the committee has identified. The organizational structure and process by which the Trinity River Restora- tion Program was intended to implement science are sound, but in practice the implementation has been difficult due to a variety of challenges (Trinity Management Council Subcommittee 2004). Nonetheless, many aspects of the structure and process used on the Trinity River could be applied to the Klamath River.

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213 CONCLUSIONS AND RECOMMENDATIONS FOuR MAJOR THEMES Four major threads or themes arose from the committee’s review of the two flow studies and their utility as scientific support for decision making: scale, the representativeness of data, connectivity, and a river-basin perspec- tive. First, the issues of water resource use, ecosystem maintenance, and preservation of endangered species are multi-scalar, so any approach to the resolution of these issues also must be at multiple scales. For example, an understanding of the annual flow of water through the river system requires an appreciation of the effects of hemispheric climate systems on a watershed several thousand square kilometers in extent operating with changes over decades. On the other hand, an understanding of the geomorphic structure of the river channel that determines the habitat conditions experienced by fish requires appreciation of physical processes that operate at the scale of a few meters and change over periods of hours to a few days. Managers must decide water allocations and dam releases within the context of the laws and agreements that have histories of a century or more but must balance those decisions against political and social values that change over decades and in a context where drought or flood conditions present monthly dilem- mas. The decisions about the water resources strongly affect local resource users, yet the fisheries resources are of much broader interest to stakehold- ers who are a national constituency. The committee found that the issue of scale of analysis pervaded its reviews of the two studies and their applica- tion and that clear specification of scale was critical to the potential success or failure of the studies. The theme of scale gives rise to the second theme, representativeness. As an example, high-quality historical flow data for the Klamath River are available for only part of the twentieth century. These data were the foun- dation for many of the conclusions that went into the construction of the two flow models, but whether or not those data are representative of the entire twentieth century was not demonstrated. The Instream Flow Study could not examine habitats along the entire length of the Klamath River, so it was necessary to select a few relatively small reaches of the river for in- tensive evaluation. If these reaches are truly representative of the full length of river, the studies have much greater value than if the reaches are less representative. Representativeness is also a thread in the history of water management of the river. During most of the history of USBR management, agency objectives have been strongly oriented toward benefits for farmers and ranchers, without representation of the interests of Native Americans in the lower Klamath River basin or of the interests of protected or valued species. Now the agency has broadened its representation of these varied interests. The third theme—connectivity (or the lack of it)—is an important char- acteristic of the Klamath River, and therefore it should be integral to the

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214 HYDROLOGY, ECOLOGY, AND FISHES OF THE KLAMATH RIVER BASIN science used to understand the river and the decision-making processes used to manage the river. Many changes that have been imposed on the river system by human activities have decreased the connectivity of its various parts. For example, upstream from the Link River Dam and the body of Upper Klamath Lake extensive marshes, formerly functionally connected to the groundwater system and the surface flows, were drained and converted to agricultural use. In the river reach above the Keno Dam, construction of a railroad embankment disconnected the Klamath River from its historical flood overflow into Lower Klamath Lake; similarly, historical overflow into the Lost River also was controlled. Connectivity also is important in the conduct of science. Science serves decision makers and the public most effectively if decision makers clearly define the purpose of the scientific investigations. If this purpose is unclear or if it changes during the course of research, the scientific products are likely to be less useful and may be wrongly or inappropriately applied. Connectivity—in the form of continuous communication—among the re- searchers themselves is crucial to the success of the scientific enterprise so that one part of the research (such as hydrology) provides inputs that are useful for another part (such as ecology). For this reason, frank and sup- portive communications between researchers are essential for outcomes of research to be useful to end-users. Connectivity among decision makers and stakeholders also is a fundamental prerequisite for the effective use of science in management. If decision makers and stakeholders lack common ground for exchange of ideas and resolution of conflicts, science is likely to be wasted, even if it is appropriate to the problem at hand, and manage- ment is likely to be fragmented. As a result, advocacy of limited perspectives is more likely to control outcomes, rather than compromises based on a sound understanding of the river’s hydrologic and ecological processes. Finally, successful science and decision making depend on a river-basin perspective. The human population of the Klamath basin is distributed over a landscape that includes parts of two states, several counties, and many communities. People living in the upper reaches of the basin have different livelihoods and expectations of Klamath River resources than the liveli- hoods and expectations of many residents of the lower reaches of the basin. The physical landscape and hydrologic and biological resources of the up- per and lower basins are different from each other in fundamental ways. It is tempting to deal with the Klamath River basin for science and decision making from at least the standpoint of the upper and lower parts, but suc- cessful science and effective decisions are most likely to be the result of viewing the whole basin and all its parts together. This view includes taking into account distant parts of the basin when considering focused problems in limited areas. In the case of the Klamath River, for example, analysis of flows without considering upstream tributaries or tributary processes along

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21 CONCLUSIONS AND RECOMMENDATIONS the main stem neglects important explanations for river behavior, because that behavior is a product of all upstream processes. NATuRAL FLOW STuDY The Natural Flow Study (USBR 2005) for the Klamath River has sev- eral admirable attributes. The river system is highly complex, and the flows of the river at the gauge near the Iron Gate Dam site reflect the influence of a complicated hydrologic system. The data sets describing stream flow that the Natural Flow Study assembled are extensive and are highly useful. The data adequately reflect the monthly seasonality of the flow system. Human activities have modified that system over substantial portions of the basin above the Iron Gate Dam gauge site, and USBR investigators included many of these modifications in their calculations. The investigators recognized the importance of marsh conversions and agricultural activities in affecting river flows and included these factors in their calculations. The documenta- tion for the Natural Flow Study (USBR 2005) is accessible to the reader and provides a straightforward explanation of what the modelers did and how they did it and provides the complete output of the research. The report also addresses important issues about the natural flow model, including brief accountings of model verification, sensitivity, and uncertainty. As a result, it has some utility in providing a generalized picture of unimpaired (natural) flows in the system and in providing a general sense of minimum flows that should be provided to ensure the safety of the basin’s fishes, although not precisely enough to lead to day-to-day management of the system. The committee concluded, however, that the Natural Flow Study was compromised by the following fundamental issues, including the choice of a basic approach to natural flows, choices of the models for calculations, and omissions of factors likely to influence river flows at the Iron Gate Dam gauge site: • The products of the Natural Flow Study, flow values for the Klam- ath River at the Iron Gate Dam site, were calculated as monthly values. However, ecological applications of the model require daily values (as discussed in more detail below in the section on the Instream Flow Study). As a result, the output of the Natural Flow Study would not have satisfied its ultimate use requirements even if the study had been executed without other errors. • The basic approach used by USBR researchers to estimate the flows of the river without the upstream influence of dams and withdrawals relied on a “black box” method of accounting for flow using a standard spreadsheet as the foundation. While such an approach allowed ready calculations and simplicity of output, the approach is not supported by a

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216 HYDROLOGY, ECOLOGY, AND FISHES OF THE KLAMATH RIVER BASIN general understanding of physical processes that influence river flows. A physically based model that has seen widespread successful use elsewhere is the USGS’s Modular Modeling System (MMS). The MMS provides greater flexibility and adaptability, and provides a firmer theoretical foundation than a straightforward accounting system. • Calculations of the fate of water in the upper basin related to evapotranspiration were not done according to the best current methods. In constructing the mass budgets needed for estimations of natural flows, the Natural Flow Study correctly recognized the importance of evapotranspira- tion in the upper basin. Greater amounts of evapotranspiration in the upper basin result in lesser amounts of stream flow at the Iron Gate Dam site, and evapotranspiration is likely to change as a result of land use and land cover, particularly the installation of agricultural practices in place of natural vegetation. The USBR used the Soil Conservation Service (SCS)1 modified Blaney-Criddle method for determining evapotranspiration from various land surfaces, but this method is now seriously outdated. A more recent and more sophisticated version of the method—the United Nations Food and Agriculture Organization’s (FAO’s) version of the modified Blaney-Criddle method—has improved accuracy for evapotranspiration calculations. The FAO modified Blaney-Criddle method has substantial data requirements, but all the required data are in the public domain and are easily accessed. Use of an up-to-date model would lend credibility to the natural flow esti- mates and would take advantage of already-collected data. • The USBR (2005) Natural Flow Study attempted to calculate flows at Iron Gate Dam without addressing several important controlling factors for those flows. Groundwater plays a critical role in the hydrologic cycle of the upper Klamath River basin. Before the advent of agriculture, the ex- change between groundwater and surface waters occurred along the courses of tributary rivers and in lake basins, sometimes through the intermediary zones of marshes and similar wetlands. After the introduction of agricul- ture, groundwater pumping and marsh drainage for fields and pastures became common, so the entire groundwater–surface-water connection was altered. Present groundwater-surface-water interactions therefore are highly unlikely to be similar to the connections that previously influenced natural flows. The Natural Flow Study did not adequately take into account the role of groundwater in the system. • More generally, the Natural Flow Study did not address the issue of changes in land use and land cover. While the study did account for marsh conversions to agriculture, there are other important land-use changes that the study did not assess. For example, the study did not assess logging for lumber and forest clearing for agriculture, but these changes in the upper 1 Now known as the Natural Resources Conservation Service.

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21 CONCLUSIONS AND RECOMMENDATIONS Klamath River basin are potentially important in influencing downstream flows. Such land-use and land-cover changes also are important along the main stem of the lower Klamath River on tributary streams, because log- ging activities on the steep slopes of the region are likely to increase sedi- ment inputs to the main stem. Remotely sensed data regarding land-use and land-cover change are available and can be analyzed using geographic information systems. Inclusion of land-use and land-cover analyses in the Natural Flow Study would have increased confidence in the resulting cal- culations, because, if such changes are important, they would reflect their influence in the model output. If the changes are unimportant, that outcome could be convincingly demonstrated. • The Natural Flow Study failed to adequately model the connection between the Klamath River and Lower Klamath Lake. Under unregulated conditions, high flows in the Klamath River main-stem channel were able to overflow a shallow divide, and water coursed into the Lost River and to Lower Klamath Lake. During low-flow conditions in the Klamath River main-stem channel, flows in the main river were not deep enough to over- flow the divide, and Lower Klamath Lake was essentially cut off from the main river channel. The availability of this “escape valve” probably was important in the pre-development river flow from Keno downstream. In the first decade of the twentieth century, the construction of a large levee to support a railroad effectively eliminated the original connection between the Klamath River and Lower Klamath Lake. Thereafter, high flows on the main stem of the Klamath River did not divert much water to the lake, leaving it in the main river. Even if all other things remained equal, the alteration of the Lower Klamath Lake connection would result in changed high flows at Keno and downstream. The hydrologic effects of this connec- tion and its consequent elimination were poorly modeled with a regression function that mixed data from years before the disconnection and after it. Because those data were at monthly intervals, the model was further made unlikely to capture important dynamics of this hydrologic interaction. The inadequate and coarse-grained modeling of such a potentially important interaction reduces the utility of the natural flows calculated by USBR (2005). • The Natural Flow Study did not adhere closely enough to standard scientific and engineering practice in the areas of calibration, testing, quality assurance, and quality control. These activities are prerequisites for confi- dence in the model products by users, including decision makers and other modelers. The committee concluded that the Natural Flow Study includes calcu- lated flows that are at best first approximations to useful estimates of such flows. The present version of the Natural Flow Study is less than adequate

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218 HYDROLOGY, ECOLOGY, AND FISHES OF THE KLAMATH RIVER BASIN for input to the Instream Flow Study and for day-to-day decision making regarding flows to benefit the listed and other anadromous fish species in the Klamath River downstream from Iron Gate Dam. To become more use- ful for meaningful decision making in flow management, the Natural Flow Study should be improved by (1) replacing the SCS modified Blaney-Criddle method for calculating evapotranspiration with a more accurate and mod- ern version, such as the FAO version of the method, using generally avail- able data; (2) including groundwater dynamics in the model in at least a general way; (3) improving the portions of the predictive model relating to land use and land cover so that changes in these variables are represented in a more complete fashion; (4) explicitly modeling the connection between the Klamath River and Lower Klamath Lake and between the Klamath and Lost rivers during flooding and recession of floods; (5) replacing the black-box accounting method based on a spreadsheet with a more robust physically based model for generating flows, such as the USGS’s MMS, or the new GSFLOW model, which couples with MMS and the groundwater model MODFLOW; (6) including an extensive investigation of high flows along with their geomorphic and ecological implications; and (7) adhering more closely to standard scientific and engineering practice by extensively validating and testing the models, while addressing issues of quality assur- ance and quality control. The set of natural-flow models used by decision makers must deal with the apparent paradox in the present model, whereby increased agricultural areas upstream produce increased river flows down- stream. Useful models either will not produce such a result, or they will lend themselves to explanation of this counterintuitive result. Finally, and perhaps most fundamentally, if the NFS is to be used to support habitat and fish-population modeling as components of IFIM, output at a daily time step is needed. INSTREAM FLOW STuDY The Instream Flow Study (Hardy et al. 2006a) used products of the Natural Flow Study as inputs to a complex modeling project designed to connect river flows and channel characteristics with habitat suitability and fish populations. Several aspects of the study are praiseworthy. The mea- surement of stream-bed topography and substrate characteristics in this study represent innovative cutting-edge methods that provided generally useful representations of the river channel. The two-dimensional hydrody- namic model in the Instream Flow Study represented an improvement over one-dimensional flow models in simulating the hydraulic aspects of physi- cal habitats. The application of two-dimensional approaches represented a willingness on the part of the investigators to engage in a highly complex and ambitious effort to deal with the hydraulic and hydrologic aspects of

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21 CONCLUSIONS AND RECOMMENDATIONS the problem of characterizing fish habitat. The study incorporated distance to escape cover, an important variable that is sometimes ignored in other studies. It leads to flow prescriptions that are closer in many aspects to natural flow patterns than the current flow regime. Model output includes comparisons of fish growth and the productivity of fish populations under current hydrologic conditions and for assumed hydrologic conditions with the flow recommendations in place. These analyses suggest some improve- ment in fish growth and production over current conditions, but they do not offer tools for evaluating tradeoffs between instream and out-of-stream uses of water. As a general perspective, the Instream Flow Study followed the modu- lar modeling process of Instream Flow Incremental Methodology (IFIM), which has seen wide application in studies of this type. Although in the committee’s judgment, the IFIM approach to river-habitat studies often is improperly used, most particularly when the PHABSIM module output is used in isolation as a static index to generate a single, flat, minimum flow and therefore not satisfactory, the authors of the study addressed each of the component modules of the IFIM as a general process. They employed bioenergetics and a fish-population model to test their results, and they tried to compare observed with model-predicted fish locations. Despite these strengths, the committee found important shortcomings in the Instream Flow Study and its use of models and data. Two shortcom- ings—use of monthly data and lack of tributary analyses—are so severe that that they should be addressed before decision makers use the outputs of the study. More fundamentally, the flow recommendations presented by the In- stream Flow Study were not directly the result of physical-habitat modeling but rather reflect a sequence of estimations and comparisons among habitat values for various life stages derived from monthly flows and estimated monthly natural-flow values, interpolations, and the selection of the lower of either the natural monthly flow or a flow computed to provide the same amount of physical habitat as the natural flow. This series of adjustments led to flow recommendations that resembled the natural hydrograph in many aspects. These steps were not the result of systematic application of the IFIM method but instead resulted from multiple decisions. The recom- mendations were indirectly derived from the models and from the highly detailed three-dimensional imaging of habitats at the site scale that were collected for the models. Although the Instream Flow Study used the PHAB- SIM module and some aspects of the temperature and salmon-population modules of the IFIM, the approach taken has unique characteristics that need further testing to evaluate them. Improvements over the simple use of the PHABSIM output as an index of habitat quality were made by Hardy et al. (2006a). The PHABSIM model has been criticized in the peer-reviewed literature,

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220 HYDROLOGY, ECOLOGY, AND FISHES OF THE KLAMATH RIVER BASIN and improved sampling and statistical approaches to modeling habitat se- lection have been proposed (for example, Castleberry et al. 1996, Williams 1999, Guay et al. 2000, Kondolf et al. 2000, Manly et al. 2002, Railsback et al. 2003, Ahmani-Nedushan et al. 2006, Anderson et al. 2006). Mem- bers of this committee hold a variety of opinions on the degree to which PHABSIM incorporates current ecological and sampling theory and on the degree to which it can be relied on, even when it is applied with careful recognition of its constraints. To the degree that any analysis (including that of Hardy et al. 2006a) relies on PHABSIM, it will need to convince others in the discipline that (1) all appropriate assumptions have been fully addressed; (2) the limitations of the model as documented in the scientific literature have been addressed; (3) both hydraulic and biological sub-models have been appropriately calibrated and tested against independent field data; and (4) the analysis recognizes that the hydraulic aspects of the habitat are but one element of a necessarily more comprehensive instream flow study. These matters are discussed in more detail below. The authors of the Instream Flow Study (Hardy et al. 2006a) were provided only with monthly flow values by the USBR in the Natural Flow Study, although daily flows were recognized to be more useful. Monthly flow values can be useful for general river-basin planning, but they are not adequate for ecological modeling for river habitats, because the monthly av- erage masks important discharge values that may exist only for a few days or even less. Sometimes these short-lived events may be over-bank flows, attended by important habitat expansions for fish, or they may be extreme low-flow events that can be detrimental to fish populations even if they last only a few days. These shorter-term variations in discharge can yield significant changes in stream hydraulics and temperature, both of which can have important ecological consequences. In either case, the very existence of critically important flow variations is masked by monthly averages, a fatal flaw. In short, planners may operate water systems on a monthly basis, but fish survive on a daily basis. The elimination of consideration of tributary processes apparently resulted from an agreement reached by basin managers not to include tribu- tary processes in the habitat studies, perhaps to simplify the engagement of stakeholders in the process. Since only the main stem of the Klamath River was subject to analysis, stakeholders with interests in tributary loca- tions would not have to deal directly with the study. However, the river is a highly integrated hydrologic and ecological system. Its tributaries give the river some of its essential characteristics and provide some of the most im- portant habitats in the basin. Detailed knowledge about the system—from the tributaries to the main channel downstream from Iron Gate Dam—is essential to the habitat analysis. The tributaries control the inflow of sedi-

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221 CONCLUSIONS AND RECOMMENDATIONS ment and add important water to the main stem, they can provide impor- tant spawning and rearing habitats and serve as refuges for fish during some low-flow periods, and they influence water quality (sometimes positively, sometimes negatively). The Klamath River is not a confined gutter for rain- water, and therefore analyzing the river without considering its tributaries is akin to analyzing a tree by assessing only its trunk but not its branches. The previous NRC (2004a) report on the Klamath River basin also emphasized the importance of understanding the lower Klamath River tributaries and including them in restoration plans, especially for coho salmon. The Instream Flow Study also exhibits modeling shortcomings. First, the study did not include important water-quality attributes, such as dis- solved oxygen levels, nutrient loadings, contaminants, and sediment con- centrations, each of which has important implications for the vitality of the fish populations of the Klamath River basin. Data on these attributes are sketchy in some cases, but at least a general assessment and discussion of the implications of water quality would have greatly enhanced the study. Second, high flows are especially important to the physical and biologi- cal processes of the Klamath River, and further analysis of their frequency, duration, and timing is essential in understanding the dynamics of the riv- er’s hydrologic, geomorphologic, and ecological processes. High flows are agents of change in the morphology and substrate of the river, over-bank flows engage floodplains as elements of habitat available to fish, and high flows entrain and rearrange sediments within the channel. River-channel morphology is not static but rather adjusts to high flows, so channel change is not continuous but rather is an event-based process keyed to high flows. Reliance on monthly flow data, as noted above, made analysis of high flows impossible in the scope of the study. Third, there was a lack of a thorough assessment of the relationship between flow-data time series and the behavior of different species and life stages and the population dynamics of coho and Chinook salmon. Such an analysis for both natural (historical) and existing flows would provide valuable insights into changes in the natural regime that have been brought about by human activities. It also would point the way toward evaluating alternative management scenarios capable of creating more natural river conditions that might lead to recovery of fish populations. Fourth, the claim that the model outcomes are accurate, as assessed by some empirical tests of fish distributions and by use of bioenergetic and the SALMOD models, impairs the utility of the Instream Flow Study’s prescrip- tions as representing the best alternative. Although the empirical tests and the bioenergetic and SALMOD model comparison to existing river-flow conditions suggest that the recommended flows offer some improvement over the current flow regime, they do not substitute for a rigorous statis- tical test of model predictions against observed distributions of fish and

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222 HYDROLOGY, ECOLOGY, AND FISHES OF THE KLAMATH RIVER BASIN sensitivity analyses of changes in fish growth and population productivity related to changes in flow regime. Statistical measures of the closeness of fit between model predictions and fish occurrence would substantially in- crease confidence in the outputs of the study. When supported by sensitivity analyses, the demonstration of modeled fish growth and productivity as a consequence of alternative flow regimes would be a useful aid to decisions about water management. Finally, there are three shortcomings in the experimental design of the Instream Flow Study: a fundamental beginning assumption about limits on salmon habitat, the representativeness of the reaches used for detailed study, and the statistical approach used to analyze the calculated set of instream flows. First, the study makes the implicit assumption that the primary limit- ing factor for the recovery of salmon is physical habitat, directly related to instream flows, but the study does not demonstrate when or even if physical habitat is a limiting factor in any of the life stages of the fishes of concern. The precise nature of any flow-related hydraulic-habitat “bottlenecks” in the population dynamics of the salmon is not demonstrated, so it is possible that temperature, dissolved oxygen, water quality, connectivity, disease, competition, or other factors are more critical to fish persistence than the hydraulic aspects of habitat are. In other words, suitable hydraulic-habitat conditions may be necessary but are not by themselves sufficient for fish persistence. Second, the study used several relatively short reaches of the Klamath River for detailed analysis and testing of the model output because it was impossible to map and analyze in detail the entire length of the river from Iron Gate Dam to the sea. The selection of representative reaches seems reasonable, but the study does not justify the selection of the reaches used in the study and does not indicate how representative they are of the unstudied reaches. A cursory analysis of the entire river might be used to determine how representative the selected reaches truly are, but at present the repre- sentativeness of the selected reaches is unknown; therefore the utility of the results also is unknown. Third, application of the Periodic Autoregressive Moving Average (PARMA) to analyze the calculated set of flows is problematic because the data were not normalized and spatial cross-correlations were not consid- ered. Also, since a PARMA (5,0) model was used, the stochastic analysis does not reflect annual autocorrelation in the hydrologic data. To avoid compromising the reliability of model predictions, stochastic models must properly incorporate spatio-temporal correlation. By missing these attri- butes, the Instream Flow Study is seriously impaired. The committee concludes that the study enhances understanding of the Klamath River basin ecosystem and the flows required to sustain it. In their present form, if they are adopted, the recommended flows resulting

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223 CONCLUSIONS AND RECOMMENDATIONS from the study should be adopted on an interim basis pending the model improvements outlined below to overcome its limitations, and a more integrated assessment of the scientific needs of the basin as a whole. The recommended flow regimes offer improvements over exiting monthly flows in that they include intra- and inter-annual variations and appear likely to enhance Chinook salmon growth and young-of-the-year production. The committee recommends that the study be improved for greater utility by (1) using daily flows as a basis for calculations; (2) taking into account habitats, water, and sediment contributions from tributaries; (3) specifically testing how representative the selected test reaches are of the entire river; (4) rigorous statistical testing of the various model outcomes to support claims of accuracy; (5) including water quality measures, sediment loadings, and contaminants in the modeling process; (6) including extended analyses of high-flow events; (7) exploring through thorough analyses of the habitat time series the potential for improving conditions for a variety of species and life stages, assuming natural and existing flows and a series of possible alternative flows; (8) developing a more comprehensive stochastic model that reflects the spatio-temporal correlation of hydrologic processes acting in the basin; and (9) using dynamic fish-population growth and production models to investigate the influence of alternative flow regimes on life cycles and stages of salmon to determine the nature of potential habitat-related bottlenecks that can constrain population growth, as well as the potential for flow-related improvements. WHAT IS THE uTILITY OF THE TWO STuDIES FOR DECISION MAKING? The committee has described the shortcomings of the Natural Flow and the Instream Flow studies as well as shortcomings imposed by the milieu in which scientific research in the Klamath River basin is planned, developed, and conducted. While these shortcomings limit potential applications of the two studies, they do not completely eliminate all potential model values. The Natural Flow Study, through its careful documentation and analysis, has provided a foundation that can be built on in future studies, and it has allowed some substantive insights to be developed. It has allowed a clearer vision of how the various parts of the Klamath River basin—especially areas above Upper Klamath Lake—interact with each other and with the Klamath River Project. Results from the Natural Flow Study facilitate the identification of additional information needs. The Instream Flow Study has made even clearer the importance of seasonal and inter-annual variability in stream flows to management and survival of the anadromous fishes of the river, and it has confirmed the apparent value of a seasonal flow pattern (hydrograph) in the Klamath River that resembles the shape of the natural

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224 HYDROLOGY, ECOLOGY, AND FISHES OF THE KLAMATH RIVER BASIN hydrograph. It has helped to delimit the ranges of variability in stream flow that might be desirable and those that might not be tolerated by the fishes. It also has provided some insights into the ways that the anadromous fishes of the Klamath River use the various habitats it provides in different flow regimes. Nonetheless, the two studies do not allow for a detailed and practical analysis of trade-offs among various flow-management regimes with respect to benefits and costs to the anadromous fishes in the river and to the agri- cultural and other interests in the basin. Before these system models can be used to guide management more specifically and with greater confidence, a more effective capacity for integrating the elements of the scientific endeavor in the basin will be needed, and the models’ more important shortcomings will need to be addressed. The most critical shortcomings of the Natural Flow Study are its inadequate treatment of linkages between the Klamath River and Lower Klamath Lake, and its provision of only monthly, rather than daily, time steps for hydrologic data. For the Instream Flow Study, the most critical shortcomings are its lack of analysis of the Klamath River’s tributaries and its use of monthly, instead of daily, flow values. CONNECTING SCIENCE WITH DECISION MAKING Connecting effective science with successful decision making for deliv- ering water to users, sustaining downstream fisheries, and protecting the populations of protected species have been problematic in the Klamath River basin. The Natural Flow Study (USBR 2005) and the Instream Flow Study (Hardy et al. 2006a) are not likely to contribute effectively to sound decision making until political and scientific arrangements in the Klamath River basin that permit more cooperative and functional decision making can be developed. The employment of sound science will require the fol- lowing elements: 1. A formal science plan for the Klamath River basin that defines research activities and the interconnections among them, along with how they relate to management and policy. 2. An independent science review and management mechanism that is isolated from direct political and economic influence and that includes a lead scientist or senior scientist position occupied by an authoritative voice for research. 3. A whole-basin viewpoint that includes both the upper and lower Klamath River basins with their tributary streams. 4. A data and analysis process that is transparent and that provides all parties with complete and equal access to information, perhaps through an independent science advisory group.

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22 CONCLUSIONS AND RECOMMENDATIONS 5. An adaptive management approach whereby decisions are played in water management with modeling efforts capable of evaluating alterna- tive flow-management schemes and with monitoring and constant assess- ment, including assessment of any management actions taken and with occasional informed adjustments in management strategies. The committee recommends that the researchers, decision makers, and stakeholders in the Klamath River basin evaluate the DOI-approved imple- mentation plan for the Trinity River Implementation Program and emulate their counterparts in the Trinity River basin in attempting to connect sci- entific efforts and decision making and that the two units coordinate their research and management for the greater good of the entire river system.