4
Natural Flow Study

INTRODUCTION

Chapter 2 described the Klamath River basin as the locale for applying models used by the U.S. Bureau of Reclamation (USBR), and Chapter 3 provided a general introduction to models. This chapter explores a specific model developed by the USBR Natural Flow Study (NFS) (USBR 2005) for estimating flows for the Klamath River at Keno (Figure 4-1).

The following pages introduce the NFS (USBR 2005) by explaining the background and objectives of the model and reviewing its history. The committee assesses the resulting study and its models by addressing the following issues:

  • Specific methods used to estimate stream flow, groundwater inflows to Upper Klamath Lake, evapotranspiration, lake levels, and the derivation of Keno gauge discharge from Link River flows using regression analysis.

  • Data, including the representativeness of the period of record, quality assurance and quality control (QA/QC), and information gaps.

  • Sensitivity, uncertainty, and error propagation.

  • Desirable analyses, alternative approaches, and follow-up.

  • Scope, context of modeling objectives and strategy, and integration into a larger plan.

Conclusions and recommendations complete the chapter, including a discussion of management implications of the NFS.



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4 Natural Flow Study INTRODuCTION Chapter 2 described the Klamath River basin as the locale for applying models used by the U.S. Bureau of Reclamation (USBR), and Chapter 3 provided a general introduction to models. This chapter explores a specific model developed by the USBR Natural Flow Study (NFS) (USBR 2005) for estimating flows for the Klamath River at Keno (Figure 4-1). The following pages introduce the NFS (USBR 2005) by explaining the background and objectives of the model and reviewing its history. The committee assesses the resulting study and its models by addressing the following issues: • Specific methods used to estimate stream flow, groundwater inflows to Upper Klamath Lake, evapotranspiration, lake levels, and the derivation of Keno gauge discharge from Link River flows using regression analysis. • Data, including the representativeness of the period of record, qual- ity assurance and quality control (QA/QC), and information gaps. • Sensitivity, uncertainty, and error propagation. • Desirable analyses, alternative approaches, and follow-up. • Scope, context of modeling objectives and strategy, and integration into a larger plan. Conclusions and recommendations complete the chapter, including a discussion of management implications of the NFS. 1

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2 HYDROLOGY, ECOLOGY, AND FISHES OF THE KLAMATH RIVER BASIN FIGURE 4-1 Keno Dam rests atop 4-1.eps sill across the Klamath River near a bedrock Keno, Oregon. The fish ladder for the dam is on the left abutment of the dam in the foreground of this view. SOURCE: Photograph by W.L. Graf, University of South Carolina, July 2006. Background and Objectives of the Natural Flow Study The USBR conducted the NFS to “estimate the effects of agricultural development on natural flows in the upper Klamath River basin” using an “estimate of the monthly natural flows in the upper Klamath River at Keno” (USBR 2005, pp. i, ix, 1). Essentially, the USBR study would pro- vide flow estimates that would be observed if there were no agricultural development such as draining of marshes and diversions of flow in the up- per Klamath basin. The following section reviews the history of the NFS, explains its relationship to Hardy et al. (2006a; also referred to here as the Instream Flow Study [IFS]), and details this committee’s interactions with the authors of the study. History of the Natural Flow Study J. Hicks (USBR Klamath Project Area Office, personal communication, 2007) provided a useful review of much of the following history of the NFS.

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3 NATURAL FLOW STUDY In 1999, Hardy completed a first-phase report containing recommendations for interim instream flows for the main stem of the Klamath River below Iron Gate Dam (Hardy 1999) (Figure 4-2). The purpose of the report was to support the ecological needs of aquatic resources, particularly anadro- mous fish species. During the early 1990s, water users and managers were entangled in disputes about the appropriation of Klamath River waters. To address this debate, the U.S. Department of Justice contracted with Utah State University (USU) in 1996 to collect information for use in the Klamath Basin Adjudication Alternative Dispute Resolution process. The Bureau of Indian Affairs (BIA) provided the funding. The following paragraphs outline the history of the NFS as determined by the committee’s hearings, conversations with participants and observers, input from J. Hicks (USBR Klamath Project Area Office, personal communication, 2007), and com- munications from T. Hardy, of Utah State University, the principal author of the IFS. Committee members visited the USBR in Denver to collect further information to support this history, which is partly summarized FIGURE 4-2 The U.S. Geological Survey stream gauge site on the Klamath River 4-2.eps immediately below Iron Gate Dam is the site for calculated natural flows and rec- ommended instream flows. The gauge site includes a cable car for sampling and a rectangular housing for data recorder and transmitter. SOURCE: Photograph by W.L. Graf, University of South Carolina, July 2006.

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4 HYDROLOGY, ECOLOGY, AND FISHES OF THE KLAMATH RIVER BASIN in Figure 1-4. Those conversations included T. Perry, a hydrologist at the USBR and the principal author of the NFS. An important aspect of the USU investigation was the estimation of unimpaired Klamath River flows, or those flows that would exist if water storage and diversion for agriculture and national wildlife refuges did not take place. The USU team proposed to estimate unimpaired flows in the Klamath River by adding together irrigation uses, consumptive use in the marshes of the wildlife refuge, and additions to flow below Upper Klamath Lake. The USU acquired consumptive-use estimates for agricultural lands above Upper Klamath Lake from the Oregon Water Resources Depart- ment and Upper Klamath Lake net inflow data and flow accretion data below Upper Klamath Lake from THE USBR. The USU team then hired contractor Phillip Williams and Associates (PWA) to use a water-routing model (MIKE 11) to estimate outflows from Upper Klamath Lake without any diversions. PWA was at the same time under contract with the USBR to evaluate the impacts of Upper Klamath Lake level regulation on water quality and endangered suckers. Also during this time, the USBR consulted with the Fish and Wild- life Service (FWS) and the National Marine Fisheries Service (NMFS) of the National Oceanic and Atmospheric Administration (NOAA) on the Klamath Project’s effects on ESA listed species. Since the NMFS had little information on coho in the Klamath River, it relied heavily on the Hardy Phase II Interim Instream Flow Needs report (Hardy and Addley 2001) rec- ommendations. Implementation of the schedules for Upper Klamath Lake surface elevations and Iron Gate Dam release schedules contained in the 2001 biological opinions resulted in the curtailment of water deliveries to the Klamath Project. Project water users suffered significant economic losses and the Klamath Project became the subject of national media. In 2001, the BIA requested that the USBR fund a revision of the PWA original hydrodynamic modeling for use in the Interim IFS. The USBR con- tracted with PWA to develop a relatively simple model to estimate historic undepleted flows for the upper Klamath River. The model PWA developed estimated the potential upper Klamath River flow based on the elimination of all agricultural depletions in the upper Klamath River basin. The model did not consider the historical size of Upper Klamath Lake, the effect of its associated marshlands, or the effects of Lower Klamath Lake or the Lost River Slough on historical river flows. The PWA group submitted its report on September 5, 2001, and THE USBR then provided it to USU. In early 2002, Oregon Water Resources Department commented to USU that the use of their consumptive-use estimates was prohibited, because the data were only to be used for the Alternative Dispute Resolution process. The BIA then requested that the USBR obtain independent consumptive use estimates. The USBR Technical Service Center (TSC) completed this project

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 NATURAL FLOW STUDY on October 10, 2002, and provided it to PWA, which finished its modeling on October 21, 2002. The results of PWA’s simplified river flow estimates were used in the development of instream flow recommendations for the Interim Instream Flow report. On November 6, 2002, T. Perry of the USBR TSC sent a Technical Memorandum to the Klamath Basin Area Office manager that identified some of the weaknesses in the simplified PWA modeling exercise (Perry et al. 2002). The memorandum also established a framework for evaluating the necessary components for an actual natural flow study. The TSC rec- ognized that a more complex study of pre-agricultural development would be necessary to estimate more accurately the actual effects of agricultural development on historical upper Klamath River flows. In late 2002, TSC initiated an intensive study to understand these agricultural effects and completed a draft in December 2004. The report was reviewed by a number of stakeholders, including agency personnel. Comments were provided on the original draft; many were implemented, along with additional model runs, for inclusion in the November 2005 final report (USBR 2005). The USBR reconsulted with the NMFS and received two new biological opinions in the spring of 2002; the new opinions again contained require- ments for stream flows and lake elevations that could result in shortages to the Klamath Project. The NMFS opinions also contained a requirement for acquisition of additional water for release to the river in amounts that increased yearly until they reached 100,000 acre-ft. For comparison, the Klamath Project’s average annual consumptive use is approximately 300,000 acre-ft. Annual expenditures to acquire this water have averaged $5.5 million. The large increase in the USBR’s funding needs generated numerous questions from government budget officials, members of Con- gress, and others. One of the most important issues was how the biological opinion requirements compared with pre-project hydrology. The USBR intended the NFS to be a more detailed study of natural flow of the upper Klamath River than the PWA consultants’ study. Neither the NFS nor the Interim IFS was designed to be used in the Endangered Species Act (ESA) consultation; however, the timing of the studies and the consultations may explain the assumption made by stakeholders that the USBR embarked upon the NFS for use in the second consultation with the NOAA. As federal officials and stakeholders became aware of the NFS, they recognized that it presented a more accurate estimate of pre-agricultural flows in the upper Klamath basin, and that it could be used in the ongoing interim instream flow work. The USBR officials thus began to redirect the focus and intent of the NFS such that it more closely coordinated with the IFS. Hardy et al. (2006a) were especially interested in the quality of the NFS

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6 HYDROLOGY, ECOLOGY, AND FISHES OF THE KLAMATH RIVER BASIN results so that they could determine whether those results were better than those of the PWA study. The instream flow team wanted hourly or at least daily flow estimates, but the USBR informed them that the data required for estimating such flows with a satisfactory degree of accuracy were unavail- able and did not provide the data. The instream flow technical team, which met frequently in Arcata, California, interacted with USBR personnel who conducted working ses- sions with team members to acquaint them with the methods used in the NFS. Members of the instream flow team suggested to the USBR that the NFS should encompass the entire river, not just the reach above Keno Dam. Team members were dissatisfied when the USBR informed them that this expansion was not possible because of time constraints. The USBR later agreed to provide natural-flow data as far downstream as Iron Gate Dam in the form of a spreadsheet showing additions to flow between the two dams, even though Iron Gate Dam is below Keno Dam, the cut-off point for the NFS. In addition, the USBR provided the interim flow team with a spreadsheet containing the estimated historical diver- sions to the Rogue Valley from Jenny Creek (a tributary above Iron Gate Dam). The combined spreadsheets represented the best available estimates of natural, undepleted additions to flow between Keno and Iron Gate dams. The only depletion from that stretch of the river that was inadvertently omitted was a diversion of 2 cubic feet per second (cfs) to 8 cfs to the City of Yreka. The instream flow team elected to use a simplified estimate of accretion rather than the data provided by U.S. Geological Survey (USGS) data and estimated diversions. The USBR noted that the flows the team chose to use were considerably higher than those provided by the USBR. When USBR staff asked the instream flow team which data they were going to use in their model for natural flow estimates for the rest of the Klamath River watershed, the team replied that it had only the USGS gauge data for impaired flows and intended to use the impaired flow data. USBR staff believed it would be inappropriate to use natural flows in the model for only one section of the river and impaired flows for the rest of the watershed. Recognizing that the instream flow team was trying to meet a deadline, USBR staff quickly estimated unimpaired flows for the Shasta, Scott, and Trinity rivers as well as some of the major creeks, and provided those data. The foregoing brief review of the origins of the NFS demonstrates that a variety of administrative forces were at work in the creation of the study. Biological opinions and the need for improved understanding of the ecological characteristics of the hydrologic system became imperative, but only after the initiation of the study. The study came to be an outgrowth of more than one objective and method, increasing the difficulty in creating a

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 NATURAL FLOW STUDY useful product. Using the output of the NFS as input to the IFS seems now, after the fact, to be a logical thing to do, but because this intended use was not apparent at the beginning of the entire process, shortcomings in such a connection were likely. As outlined later in this chapter, the final product of the NFS did make some contributions to scientific understanding of the hydrology of the Klamath River. There were also some shortcomings that might have been avoided if there had been greater coordination among hydrologic, ecological, and operations researchers at the beginning of the NFS. Meeting with the National Research Council Committee A group of members of the NRC committee and NRC staff met with USBR staff in Denver on November 20, 2006. Thomas Perry, USBR Techni- cal Lead, Jon Hicks, of the USBR Klamath Basin Area Office (KBAO), and other USBR personnel were also present. Perry’s PowerPoint presentation and comments provided much of the information to the group. During Perry’s PowerPoint presentation, he emphasized that the prime directive to the NFS team was “do not underestimate natural flows.” Dur- ing his discussion of the sensitivity analysis, he showed that the model pro- duces an increase in flow at the Keno gauge when the consumptive use in the upper Klamath basin is increased. In other words, more water used by agriculture means more water going into the Klamath River. Perry posited that this phenomenon had something to do with “water limiting” condi- tions for evapotranspiration in Upper Klamath Lake. This proposition is discussed in a subsequent section of this chapter. Natural Flow Study General Approach The USBR used a water-budget approach to estimate natural flows at the Keno gauge. As stated by USBR (2005, p. ix): The approach was to evaluate the changes of agriculture from predevel- opment depletions, estimate the effects of these changes, and restore the water budget to natural conditions by reversing the effects of agricultural development. Records used in this empirical assessment were derived from both stream gaging flow histories and from climatological records for sta- tions within and adjacent to the study area. The emphasis was on the effects of agricultural development; other changes, such as changes in forest cover, were not assessed (USBR 2005, p. xiii). The USBR first developed a reasonably accurate conceptual model (Figure 4-3) to identify all the significant components of the basin water budget. The model was useful for identification and the subsequent quan-

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8 HYDROLOGY, ECOLOGY, AND FISHES OF THE KLAMATH RIVER BASIN 4-3.eps FIGURE 4-3 Conceptual model of the NFS. SOURCE: USBR 2005. fixed image tification of gains and losses associated with the process of “naturalizing” the current conditions. The NFS produced results of the water-budget approach given as monthly flows at the Link River gauge and the Keno gauge on the Klamath River. The Keno gauge flows were estimated from a regression equation

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 NATURAL FLOW STUDY between the Link River gauge and the Keno gauge. The period of record was 52 years, from 1949 through 2000. A longer period was not included because of the generally unreliable data prior to 1949 and the lack of any data at the start of the study that was newer than 2000 (T. Perry, USBR, personal communication, 2006). The NFS used the following generalized steps (USBR 2005): • Compute naturalized flows from the major tributaries—the Sprague, Williamson, and Wood rivers—to Upper Klamath Lake. • Compute groundwater inflows into Upper Klamath Lake. • Develop natural stage-storage and stage-discharge relationships for Upper Klamath Lake. • Perform a detailed water-budget analysis of Upper Klamath Lake using naturalized inflows, natural (predevelopment) evapotranspiration from marshes surrounding Upper Klamath Lake and the open water surface within Upper Klamath Lake and the stage-storage, stage-discharge relation- ships to compute naturalized outflows from Upper Klamath Lake to yield naturalized flows at the Link River gauge. • Develop and use a regression equation to compute naturalized flows at the Keno gauge using naturalized flows at the Link River gauge. The study implemented the water-budget approach using an Excel spread- sheet and customized computational modules developed specifically for the spreadsheet. Other models were not used because “this study is unique” (USBR 2005, p. xii). METHODS FOR THE NATuRAL FLOW STuDY Stream Flow The NFS used a water-budget approach to compute predevelopment flows in the upper Klamath basin. The NFS determined natural flows at the location corresponding to the current Keno gauge by developing a regres- sion equation between Link River and Keno gauges. The basic water-budget approach attempts to “naturalize” flows by adjusting the gauged stream flows to account for losses and gains due to such changes in the basin as agricultural practices and loss of natural marshes along the streams due to watershed development. Computation of the naturalized flows from the tributary watersheds of Upper Klamath Lake required the adjustment of gauged flows using the following equation: Natural flow = (gauged flow) + (crop net consumptive use) – (reclaimed natural marshland net evapotranspiration). (4-1)

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100 HYDROLOGY, ECOLOGY, AND FISHES OF THE KLAMATH RIVER BASIN Although major tributaries have historical records, their records often have missing values. The NFS used a correlation analysis to restore such missing values and create complete gauge records. At other locations where gauged flows are unavailable, techniques of stream flow estimation for ungauged basins have been used. Figure 4-4 is a flowchart of the approach used for naturalizing stream flows. Groundwater Subsurface inflow to Upper Klamath Lake is a significant unmeasured component of the lake’s water budget (USBR 2005, Attachment E). As- sessment of this water-budget component is difficult. The ongoing USGS- Oregon Department of Water Resources study, due to be completed in 2007 or 2008, should help to quantify the uncertainty, which in turn will allow better understanding of the significance of subsurface inflow and its impact on model outcomes. One of the key elements of this study is a groundwater flow model, which can be used to estimate groundwater-lake interactions. The NFS used estimates developed by Hubbard (1970), who in turn based his estimates on a water budget for Upper Klamath Lake over a 2- year period, 1965-1967. The amount of water required to balance the lake’s water budget was an “input” term, which Hubbard assumed to be due to groundwater inflow. This is the “derived groundwater inflow” used by the NFS (USBR 2005, Attachment E). In this approach, one is simply solving for the unknown in the water budget. This approach has the disadvantage that the unknown term, a residual, contains all the cumulative errors. The terms Hubbard assumed to be “known” (calculable) include surface-water inflow, precipitation, evapotranspiration (calculated using the the Blaney- Criddle method); open-water evaporation, and storage. Hubbard used an incorrect relationship for the area capacity of Upper Klamath Lake and for inundated marsh areas, because he incorrectly referenced USGS elevations to the USBR datum. The NFS corrected those two shortcomings. The corrected USBR estimates of groundwater accrual to Upper Klam- ath Lake averaged about 19,500 acre-ft per month, assumed to emanate from the regional aquifer. The NFS adjusted the groundwater inflows for a climate signal, based on the inferred climate-influenced discharge from the deep regional aquifer in the region of the lake (Gannett et al. 2003). In several of the upper Klamath basin watersheds, groundwater pump- ing is significant, from either the regional confined aquifer (Sprague and Williamson valleys) or the valley-fill alluvial aquifer (Wood River valley). M. Gannett (USGS, personal communication, 2007) reported that in 2000, total pumpage in the upper Klamath basin was about 150,000 acre-ft, or about 10% of the average annual discharge at Iron Gate Dam. In the case of the regional aquifer, the NFS assumed that the deep

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101 NATURAL FLOW STUDY FIGURE 4-4 Flowchart of natural stream flow methods used for computing natural 4-4.eps inflows to Upper Klamath Lake. SOURCE: USBR 2005, Attachment B. fixed image—needs better original file

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124 HYDROLOGY, ECOLOGY, AND FISHES OF THE KLAMATH RIVER BASIN In this effort, a Natural System Model (NSM) was developed to simulate the hydrologic response of the pre-drainage Everglades. The NSM does not attempt to simulate the pre-drainage hydrologic data that existed prior to human-influenced changes in south Florida, but rather it uses more recent climatic data to simulate the pre-drainage hydrologic response to current hydrologic input. The use of recent input data, for example, rainfall, poten- tial evapotranspiration, and tidal and inflow boundary conditions, allows for a meaningful comparison between the current managed system and the natural system under identical climatic conditions. Information from the managed system models is used to parameterize the NMS. Using an approach similar to the NSM used in Florida’s Everglades is preferable to the naturalization of historical flows used in the NFS, but the ability to calibrate the managed model used to derive the NSM does not ensure a fully calibrated model under natural conditions. The use of param- eters calibrated using managed-system models for simulating flows under unmanaged conditions includes some inherent uncertainties that must be considered when such flows are used in any applications. Evapotranspiration The scientific literature provides extensive evidence to suggest that the SCS modified Blaney-Criddle method is one of the least accurate methods for estimating evapotranspiration (see review in the evapotranspiration portion of the methods section above). One justification for selecting this method was the insufficient data for other more accurate methods (for example, the Penman-Monteith approach [Monteith 1965]) for the se- lected period of record. A remarkably more accurate method that does not require as many data as those required for the Penman-Monteith method is the Food and Agriculture Organization (FAO) modified Blaney-Criddle equation (Cuenca 1989, Jensen et al. 1990). Based on statistical analyses of data from many locations worldwide, the FAO modified the SCS modified Blaney-Criddle formula as follows: ETr = A + B[P(0.46T + 8.13)], (4-3) where ETr is the reference crop (grass) evapotranspiration (mm/day), P is the percent of annual sunshine during month on a daily basis, T is the mean temperature in degrees C, and A and B are climatic calibration coefficients (Cuenca 1989). The coefficients A and B are functions of minimum relative humidity, RHmin, the ratio of actual to maximum possible sunshine hours, n/N, and daytime wind velocity, Uday. Although the inclusion of these pa- rameters to estimate A and B appear to require a great deal of additional data, Cuenca (1989) suggested that approximate values in the ranges of

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12 NATURAL FLOW STUDY low, medium, and high can be applied. These approximate ranges of RHmin and Uday are available from detailed measurements at AgriMet stations (USBR 2007a). Recent regional reanalysis of historical climatic data through the joint effort of National Center for Environmental Prediction (NCEP) and the Na- tional Center for Atmospheric Research (NCAR) has made unprecedented meteorological data available, allowing the use of more accurate combina- tion methods for estimation of evapotranspiration. For example, the North America Regional Reanalysis (NARR) data set (NCEP 2007) provides all the data necessary to apply the Penman-Monteith equation for estimating reference crop evapotranspiration. Another data set has been developed by using the NOAA Land Data Assimilation System (NCEP 2006), which is a 51-year (1948-1998) set of hourly land-surface meteorological data used to execute the NOAA land-surface model, all on the 1/8th degree (about 12 km) grid of the North American Land Data Assimilation System (NLDAS). In this model, the surface data include air temperature, humidity, surface pressure, wind speed, and surface downward short-wave and long-wave radiation, all derived from the National Center for Environmental Predic- tion–National Center for Atmospheric Research (NCEP-NCAR) Global Reanalysis. To show how these data could be used for evapotranspiration estima- tion, the NARR data downloaded for a nine-point grid near Upper Klamath Lake (Figure 4-14) demonstrate how these data could support evapotrans- piration estimation. Figure 4-15 is a box and whisker plot showing how the reference evapotranspiration can be calculated for grass using the Penman-Monteith equation for one of the points shown in Figure 4-14. The daily reference evapotranspiration values computed using climatic data available from regional reanalysis project can easily be used for hydrologic modeling in the Klamath basin. However, when using regionalized data, some local calibration of reference evapotranspiration may be necessary to account for localized effects within the basin. Agricultural Development Perry (2006) reported that during the sensitivity analysis of the NFS, the model produced an increase in flow at the Keno gauge when the con- sumptive use in the upper Klamath basin increases. In other words, more water used by agriculture means more water going into the Klamath River. Perry posited that this phenomenon had something to do with “water limit- ing” conditions for evapotranspiration in Upper Klamath Lake, but offered no further explanation. Although such a result is not impossible, it is at least counterintuitive, and it should be explored and explained completely,

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126 HYDROLOGY, ECOLOGY, AND FISHES OF THE KLAMATH RIVER BASIN FIGURE 4-14 NARR grid points near Upper Klamath Lake used for downloading 4-14.eps climatic data for evapotranspiration estimation. because it could call into question the underpinnings of the entire model and lead to the unconfirmed conclusion that additional agricultural devel- opment would actually increase upper Klamath basin flows. Groundwater Inflows to Upper Klamath Lake The NFS estimated inflow to Upper Klamath Lake as the residual in the water-budget equation. This approach, while simple, lumps all the errors into the residual. The USBR did not attempt to verify that its estimates were reasonable, which it could have done by calculating inflows to the lake us- ing a Darcy’s Law approach and the existing potentiometric data. Gannett (2007) also presented some preliminary quantitative information on the groundwater flow in the upper Klamath basin. Changes in Land Cover The study made no attempt to consider the effects of changing land cover in the upper Klamath basin, especially the loss of forest land and its

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12 NATURAL FLOW STUDY FIGURE 4-15 Box and whisker plots of monthly evapotranspiration (summed 4-15.eps from daily data) estimated by using the NARR meteorological data for grid point fixed image—rules < 0.5 pt number 5 (Figure 4-14) and the Penman-Monteith equation. conversion to other non-forest uses. These changes would presumably af- fect the infiltration and runoff in the upper-basin watersheds, which could in turn affect the stream flow. The development of a detailed land-cover history of the upper basin watershed using readily available aerial photog- raphy supplemented with satellite imagery would enhance the reliability of the resulted estimated flows. Interactions with Lower Klamath Lake Perry (2006) indicated that simulation of Lower Klamath Lake needs to be revisited. The NFS concluded that Several attempts were made to model this complex system using a digital representation in Excel of the lake/river physical interaction. Because of the complexity of the hydraulics, and the need for detailed data, this modeling is not possible at this time. A correlation approach was used to estimate Keno flows at the outfall of the LKL [Lower Klamath Lake] system. Mea- sured data for the period of October 1904 through September 1918 for the Link River and Keno gauges were used (USBR 2005, Attachment F, pp. 15-16).

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128 HYDROLOGY, ECOLOGY, AND FISHES OF THE KLAMATH RIVER BASIN Regression modeling is inadequate to simulate the complex interactions between the river and Lower Klamath Lake, so this task will likely require a complex modeling effort. THE NATuRAL FLOW MODEL: CONSEquENCES The stated purpose of the NFS was to “estimate the effects of agricul- tural development on natural flows in the Upper Klamath River Basin” (USBR 2005, Preface). Essentially, the USBR’s study provided flow estimates that would be observed if there was no agricultural development in the up- per Klamath basin. To quote further, The approach was to evaluate the changes of agriculture from predevel- opment depletions, estimate the effects of these changes, and restore the water budget to natural conditions by reversing the effects of agricultural development. Records used in this empirical assessment were derived from both stream gaging flow histories and from climatological records for sta- tions within and adjacent to the study area. (USBR 2005, p. ix) Also, due to the effects of the flows required by the NMFS biological opinions, government officials and others saw the NFS as a means to com- pare pre-development flows with those required by the biological opinions and effect comparisons between the two: It seems to be a common belief that the NFS was produced to counter the flow recommendations of the Hardy Phase II report and/or the NOAA biological opinion. As stated previously, the NFS was originally developed as a means of comparing biological opinion flows to natural conditions because that information was requested by federal officials and others. (J. Hicks, USBR Klamath Project Area Office, personal communication, 2007) Hicks continued with a discussion of the connections among the NFS, ESA considerations, and operation of the irrigation project: Members of Dr. Hardy’s technical team asked if Reclamation intended to use the NFS to define the maximum releases to the river from the Project with the goal being to mimic the natural hydrograph. An understanding of ESA consultation procedures illustrates that this was and is not the case. In ESA consultation, a required step is to describe the baseline conditions. The baseline is defined in the implementing regulations as current condi- tions and includes past actions and modifications to the ecosystem. The proposed action, here, continued operations of the Klamath Project, is then compared to the baseline to determine the affect to the species. Any nega- tive effect of the action on listed species is in addition to the conditions described in the baseline. The natural flows, prior to agricultural develop-

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12 NATURAL FLOW STUDY ment, are not relevant to the baseline or to the effect Project operations will have on the listed species under the current conditions. The analysis of Project effects is not a comparison of natural conditions versus with- Project conditions, it is a comparison of baseline to baseline plus Project affects and what the consequences are for the continued existence of the listed species. (J. Hicks, USBR Klamath Project Area Office, personal com- munication, 2007) It is premature to speculate upon the future uses of the NFS model for future management or policy decisions. The USBR invested heavily in the development of the model, so it would seem unlikely that it will be perma- nently retired: As for other potential decisions, the NFS model is a tool, and like any tool, you must first determine if it is appropriate for use in the particular management or policy decision at hand. It is not prudent to speculate what future management or policy decisions may arise and if the NFS would inform them or not, however, it will be evaluated on a case by case basis to determine when and if it applies to specific decisions and only be used when appropriate. (J. Hicks, USBR Klamath Project Area Office, personal communication, 2007) The NFS model has already been applied to situations beyond its in- tended use. It is likely to see further use in studies related to the Klamath Project and listed species so that modifications and enhancements to the model should be made with these potential applications in mind. CONCLuSIONS AND RECOMMENDATIONS In conducting the NFS, the USBR faced a daunting task: unravel the complicated natural and artificial “plumbing” of the upper Klamath basin, and from that knowledge estimate the degree to which flows of the Klamath River at Keno Dam would approximate those prior to agricultural develop- ment. In addition to the intellectual challenges, the NFS faced time, money, and personnel constraints. Additionally, the USBR conducted the study in a highly charged at- mosphere in which virtually every person and stakeholder group in the Klamath basin, as well as many outside the basin, had an enormous stake. Almost from the beginning, many misunderstood the initial raison d’être for the study. Its original purpose did not include providing input for the model under development by the Instream Flow Phase II Study. However, the NFS eventually served this purpose, because little else was available and the IFS also was under tight deadlines. Some groups wanted the USBR to extend its NFS to the entire Klamath basin, and expressed disappointment

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130 HYDROLOGY, ECOLOGY, AND FISHES OF THE KLAMATH RIVER BASIN when that proved unfeasible. The USBR was able to provide the IFS group with “quickly estimated unimpaired flows” for the major creeks as well as the Scott, Salmon, and Trinity rivers. There are some notable features of the NFS model: • The conceptual model used for the development of the water bud- get is thorough and includes attention to detail. • The seasonality of the simulated natural system flows is adequate at the monthly scale. • The model is a good representation of a complicated hydrologic system with pronounced anthropogenic modifications, given the time, per- sonnel, and cost constraints and the contentious atmosphere. • The model captures decadal variations in precipitation and runoff that occur independently of the modified system. • The model is constructed on a relatively user-friendly platform (Excel spreadsheet) and its modular construction makes it easy to modify and use. These and other features of the model lead the committee to conclude that 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. These topics are discussed in more detail in the final section of the chapter. Specific conclusions and recommendations follow. Conclusion 4-1. The model generally lacks adequate calibration and test- ing. Overall, QA/QC were not performed in accordance with available scientific and practical standards. Recommendation 4-1. If the current modeling approach is retained, cali- bration, testing, and QA/QC need to be performed adequately. Conclusion 4-2. Treatment of error, sensitivity, and uncertainty did not receive adequate attention and was not performed at the level required for informed decision making. Recommendation 4-2. If the current modeling approach is retained, docu- ment, report, and illustrate the sensitivity analysis of the water-budget model and develop uncertainty estimates of simulated natural flows. Conclusion 4-3. Lower Klamath Lake was integrally linked to the main- stem Klamath River. High flows in the Klamath River overflowed into

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131 NATURAL FLOW STUDY Lower Klamath Lake, effectively attenuating peak flows before they reached the Keno gauge. During the flood recession, there was some “return flow” from Lower Klamath Lake into the main-stem Klamath River, and during low-flow periods the two were disconnected. This natural arrangement ended with the construction of a railroad grade in the early twentieth cen- tury that prevented river overflow into the lake, thereby increasing peak flows in the main stem. Simulation of the river’s natural flow should there- fore include interactions with the lake. Recommendation 4-3. If the current modeling approach is retained, simu- lation of interaction between the Klamath River and Lower Klamath Lake is inadequately represented. The present NFS attempts to capture the effect of these complex river-Lower Klamath Lake interactions using only a sim- ple regression to relate flows at the Link River gauge to flows at the gauge below Iron Gate Dam on a monthly time step. A more rigorous model of natural flows should incorporate a hydraulically based sub-model of the Klamath River-Lower Klamath Lake connection on a daily time step. Conclusion 4-4. Land cover influences hydrologic processes in the upper Klamath basin, hence influences the flows downstream. The NFS does not adequately account for changes in land use and land cover in the watershed, limiting confidence in the model’s ability to simulate accurately downstream flows. Recommendation 4-4. If the current modeling approach is retained, the NFS model should account for the effects of the change in upper Klam- ath basin forest cover on Keno gauge flows by extending its analysis to historical aerial photography, satellite imagery, ground photographs, and documentary descriptions. Conclusion 4-5. The prediction of the NFS that flow in the Klamath River at the Keno gauge will increase if irrigated acreage upstream increases is surprising and is not explained. Recommendation 4-5. The prediction by the model that an increase in agricultural development in the upper Klamath basin produces an increase in flow at Keno gauge is puzzling. The reasons for this model result should be explored, its implications for the model generally should be considered, and the phenomenon should be investigated further and explained. Conclusion 4-6. The SCS Blaney-Criddle method for estimation of evapo- transpiration, a key component of the NFS, is not the best method available and its use in the NFS likely led to inaccurate results.

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132 HYDROLOGY, ECOLOGY, AND FISHES OF THE KLAMATH RIVER BASIN Recommendation 4-6. If the current modeling approach is retained, the USBR should consider replacing the SCS modified Blaney-Criddle method with a more accurate method, such as the FAO version of the Blaney- Criddle method. Conclusion 4-7. The results of the NFS illustrate the complexity of hydro- climatic processes within the upper Klamath River basin and show that the seasonal patterns of runoff and storage are strongly influenced by the collective effects of land use and water-management practices. It is appar- ent that the model captures the longer-term (decadal scale) variations in precipitation and runoff that occur independently of the modified system. The modeled stream flows reflect conditions for the period 1949-2000, which may or may not be representative of the hydrology of the basin. The limited data available for the first half of the twentieth century suggest that precipitation and runoff in the upper Klamath basin were lower then than they were in the latter half of the twentieth century. Future conditions of precipitation and runoff are unknown, thus the volume of water available for agricultural or municipal use, or instream flows, could be significantly different from the flows developed in the NFS. Recommendation 4-7. Develop a fully distributed precipitation-runoff- groundwater model for the upper Klamath River basin. This type of model is already under development in parts of the basin (Matanga et al. 2004, Hay et al. 2005). Conclusion 4-8. The monthly time step used in the water-budget model is inconsistent with the daily data required for the development of instream flows at Iron Gate Dam and at downstream locations. A water-budget model like the one used in the NFS is inappropriate for simulation of naturalized flows on a daily basis. The NFS also was limited to the upper Klamath basin, but the IFS requires naturalized flows for the entire Klamath basin. Recommendation 4-8. Use an integrated framework for the models and their linkages for the entire Klamath basin. Develop a rigorous, physically based precipitation-runoff-groundwater model for the entire basin that can be calibrated using more recent data. The calibrated model can subse- quently be used estimate flows under natural conditions. MANAGEMENT IMpLICATIONS OF THE NATuRAL FLOW STuDY The basic results of the NFS are sets of simulated mean monthly and mean annual flows at Link River and at Keno in cubic feet per second,

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133 NATURAL FLOW STUDY along with simulated monthly water surfaces for Upper Klamath Lake, un- der natural conditions. The monthly flows are also expressed as discharges with exceedance values, so that the results indicate values expected to occur greater than 10% of the time, 20% of the time, and so forth up, to 90% of the time. The importance of these values is that, taken together, they represent a statistical picture of flows expected at Link River and Keno if there had been no upstream agriculture and no control by dams. The USBR intended that these flows serve as a representation of the natural flow of the river, although special efforts were made not to underestimate such flows. As such, they might serve as guidance to managers of the system in that they potentially reflect limits of flow below which managers probably should not go to avoid threatening the existence of the system’s fish species, and above which they need not go to protect the species. The implications of the model investigations that produced the simu- lated hydrologic features of the basin are mixed. From a positive perspec- tive, the results define monthly “natural” variation that managers might reasonably expect, absent their own activities. The monthly variation de- picted by the model represents a simulated picture of the conditions under which the biological community of the river evolved and provides a back- drop for assessing the degree to which the present regulated flow regime departs. The flows also provide a general view of the total amounts of water involved in the river and lake regime, with about 1.4 million acre-ft annu- ally flowing out of the lake on the average. The NFS reasonably captures the decadal variations in flows in the system that are likely to have occurred in the absence of upper-basin de- velopment and the installation of dams. These decadal variations, like the monthly variations, are likely to have been ecological features of the bio- logical community as it evolved in the lower river. These variations imply that in the regulated system, some decadal fluctuation in flows is reason- able, and that a completely unchanging regime imposed by engineering structures would not reflect the natural regime. However, the internal workings of the model in the NFS include several computational shortcomings that imply limits to its use. For example, sen- sitivity analyses produce unexpected and unexplained responses to changes in the consumption of water in the upper basin. According to the sensitivity analysis, shared with this committee, the flows out of Upper Klamath Lake increase when the agricultural land use in the upper basin is increased. This is a surprising result, discussed above, and at a minimum, it deserves further study and explanation. In addition, the method for determining evapotranspiration in the model fails to take advantage of recent advances and readily available data that would sharpen predictions. These issues imply that the natural flow model produces results that probably cannot be used as a precise replication

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134 HYDROLOGY, ECOLOGY, AND FISHES OF THE KLAMATH RIVER BASIN of natural flows and that the individual numbers generated by the study are not firm, irrefutable values. This committee found inadequacies in basic model-building protocol in the construction and refinement of the natural flow model. The model lacks adequate testing, calibration, error analysis, and sensitivity assessment, and it does not adequately address issues related to uncertainty. Although the simulated natural flows have been compared with a short period of earliest gauged records available, the particular approach used for “naturalizing” managed flows does not allow a formal calibration of the model. These shortcomings imply that managers of the biological resources of the basin may use the results of the model in a general way as a form of guidance for the broad characteristics of the natural flow regime, but they cannot use the exact values produced by the study as a template for developing a flow regime with much confidence. Decision makers do not have the advantage of knowing the degree of potential error in the reported monthly flows, values that lack error envelopes or other expressions of uncertainty. The model is a general representation, and because its output is in monthly time steps, it is not capable of generating the daily time step needed for a completely effective instream flow model to be used in any ecological model downstream. As described in considerations of the IFS in the follow- ing chapter, this limitation has a ripple effect that limits the utility of the instream flow recommendations. Finally, the current model is severely restricted for two general reasons. First, the basin and its biota have changed so much in the past century that the implications for the fishes of restoring “natural flows” are not clear. In addition to changes in vegetation and in the species composition of the animals in Upper Klamath Lake, Klamath River, and their tributaries, the genetic makeup and abundance of the anadromous fishes of the river have changed as well. As a result, it is by no means certain that restoring a natural hydrologic regime to the basin would lead to the distribution, abun- dance, and species composition that characterized it before the project was initiated. Second, the model does not treat the tributaries of the Klamath River, and they are and have been an essential part of the environments of the anadromous fishes. Without understanding their ecological and hydrological condition and dynamics, it is not possible to understand the ecological and hydrological condition and dynamics of the river. A modified version of the NFS model, incorporating suggestions made earlier, could have management utility. It could be used as a template for a model of the present-day system. Such a model could be used to simulate “What if?” scenarios, test certain hypotheses, and demonstrate to stake- holders the implications of assorted management decisions and stakeholder choices. Since the NFS model is built upon a familiar, user-friendly platform (Excel), a modified model might find wide use among stakeholders.