Groundwater Simulation and Management Models for the Upper Klamath Basin, Oregon and California

U.S. Geological Survey (USGS) | May 5th, 2012

The upper Klamath Basin encompasses about 8,000 square miles, extending from the Cascade Range east to the Basin and Range geologic province in south-central Oregon and n

The upper Klamath Basin encompasses about 8,000 square miles, extending from the Cascade Range east to the Basin and Range geologic province in south-central Oregon and northern California. The geography of the basin is dominated by forested volcanic uplands separated by broad interior basins. Most of the interior basins once held broad shallow lakes and extensive wetlands, but most of these areas have been drained or otherwise modified and are now cultivated. Major parts of the interior basins are managed as wildlife refuges, primarily for migratory waterfowl. The permeable volcanic bedrock of the upper Klamath Basin hosts a substantial regional groundwater system that provides much of the flow to major streams and lakes that, in turn, provide water for wildlife habitat and are the principal source of irrigation water for the basin’s agricultural economy. Increased allocation of surface water for endangered species in the past decade has resulted in increased groundwater pumping and growing interest in the use of groundwater for irrigation. The potential effects of increased groundwater pumping on groundwater levels and discharge to springs and streams has caused concern among groundwater users, wildlife and Tribal interests, and State and Federal resource managers. To provide information on the potential impacts of increased groundwater development, and to aid in the development of a groundwater management strategy, the U.S. Geological Survey, in collaboration with the Oregon Water Resources Department and the Bureau of Reclamation, has developed a groundwater model that can simulate the response of the hydrologic system to these new stresses. The groundwater model was developed using the U.S. Geological Survey MODFLOW finite-difference modeling code and calibrated using inverse methods to transient conditions from 1989 through 2004 with quarterly stress periods. Groundwater recharge and agricultural and municipal pumping are specified for each stress period. All major streams and most major tributaries for which a substantial part of the flow comes from groundwater discharge are included in the model. Groundwater discharge to agricultural drains, evapotranspiration from aquifers in areas of shallow groundwater, and groundwater flow to and from adjacent basins also are simulated in key areas. The model has the capability to calculate the effects of pumping and other external stresses on groundwater levels, discharge to streams, and other boundary fluxes, such as discharge to drains. Historical data indicate that the groundwater system in the upper Klamath Basin fluctuates in response to decadal climate cycles, with groundwater levels and spring flows rising and declining in response to wet and dry periods. Data also show that groundwater levels fluctuate seasonally and interannually in response to groundwater pumping. The most prominent response is to the marked increase in groundwater pumping starting in 2001. The calibrated model is able to simulate observed decadal-scale climate-driven fluctuations in the groundwater system as well as observed shorter-term pumping-related fluctuations. Example model simulations show that the timing and location of the effects of groundwater pumping vary markedly depending on the pumping location. Pumping from wells close (within a few miles) to groundwater discharge features, such as springs, drains, and certain streams, can affect those features within weeks or months of the onset of pumping, and the impacts can be essentially fully manifested in several years. Simulations indicate that seasonal variations in pumping rates are buffered by the groundwater system, and peak impacts are closer to mean annual pumping rates than to instantaneous rates. Thus, pumping effects are, to a large degree, spread out over the entire year. When pumping locations are distant (more than several miles) from discharge features, the effects take many years or decades to fully impact those features, and much of the pumped water comes from groundwater storage over a broad geographic area even after two decades. Moreover, because the effects are spread out over a broad area, the impacts to individual features are much smaller than in the case of nearby pumping. Simulations show that the discharge features most affected by pumping in the area of the Bureau of Reclamation’s Klamath Irrigation Project are agricultural drains, and impacts to other surface-water features are small in comparison. A groundwater management model was developed that uses techniques of constrained optimization along with the groundwater flow model to identify the optimal strategy to meet water user needs while not violating defined constraints on impacts to groundwater levels and streamflows. The coupled groundwater simulation-optimization models were formulated to help identify strategies to meet water demand in the upper Klamath Basin. The models maximize groundwater pumping while simultaneously keeping the detrimental impacts of pumping on groundwater levels and groundwater discharge within prescribed limits. Total groundwater withdrawals were calculated under alternative constraints for 2 Groundwater Simulation and Management Models for the Upper Klamath Basin, Oregon and California drawdown, reductions in groundwater discharge to surface water, and water demand to understand the potential benefits and limitations for groundwater development in the upper Klamath Basin. The simulation-optimization model for the upper Klamath Basin provides an improved understanding of how the groundwater and surface-water system responds to sustained groundwater pumping within the Bureau of Reclamation’s Klamath Project. Optimization model results demonstrate that a certain amount of supplemental groundwater pumping can occur without exceeding defined limits on drawdown and stream capture. The results of the different applications of the model demonstrate the importance of identifying constraint limits in order to better define the amount and distribution of groundwater withdrawal that is sustainable.

Guidelines for salmonid passage at stream crossings

National Marine Fisheries Service (NMFS) | August 20th, 2013

This document provides guidelines for design of stream crossings to aid upstream and downstream passage of migrating salmonids. It is intended to facilitate the design of

This document provides guidelines for design of stream crossings to aid upstream and downstream passage of migrating salmonids. It is intended to facilitate the design of a new generation of stream crossings, and assist the recovery of threatened and endangered salmon species. These guidelines are offered by the National Marine Fisheries Service, Southwest Region (NMFS-SWR), as a result of its responsibility to prescribe fishways under the Endangered Species Act, the Magnuson-Stevens Act, the Federal Power Act, and the Fish and Wildlife Coordination Act. The guidelines apply to all public and private roads, trails, and railroads within the range of anadromous salmonids in California.

Hydrology and Hydrodynamics on the Sacramento River Near the Fremont Weir, California—Implications for Juvenile Salmon Entrainment Estimates

U.S. Geological Survey (USGS) | November 9th, 2018

Estimates of fish entrainment on the Sacramento River near the Fremont Weir are a critical component in determining the feasibility and design of a proposed notch in the

Estimates of fish entrainment on the Sacramento River near the Fremont Weir are a critical component in determining the feasibility and design of a proposed notch in the weir to increase access to the Yolo Bypass, a seasonal floodplain of the Sacramento River. Detailed hydrodynamic and velocity measurements were made at a river bend near the Fremont Weir in the winter and spring of 2016 to examine backwater conditions and estimate the hydraulic entrainment zone, a zone where fish would be predicted to be entrained into the notch. Secondary circulation near the river bend was shown to shift the velocity and discharge distributions toward the outside of the bend. Variability in the stage-discharge relation was shown to be the biggest source of uncertainty in determining the location of the hydraulic entrainment zone. Outflow from the Sutter Bypass and high flow on the Feather River resulted in backwater conditions near the Fremont Weir about 25 percent of the time over the 27-year period from April 1990–April 2017. Velocity measurements used to estimate the critical streakline position (the outer edge of the hydraulic entrainment zone) were not made over a sufficient range of conditions to explicitly quantify the variability in the location of the critical streakline. The variability in the critical streakline position was therefore represented stochastically with a random effects model. The estimated position of the critical streakline and the random effects model are input parameters used in a simulation designed to estimate fish entrainment over a 15-year period. The estimates of the critical streakline and likely fish entrainment could be much improved with velocity measurements over a broader range of stage and discharge conditions. 

Hydrology, Ecology, and Fishes of the Klamath River Basin (2008)

National Academy of Sciences (NAS) | January 1st, 2008

The Klamath River basin, which spans parts of southern Oregon and northern California, has been the focus of a prominent conflict over competing uses for water. Manag

The Klamath River basin, which spans parts of southern Oregon and northern California, has been the focus of a prominent conflict over competing uses for water. Management actions to protect threatened and endangered fish species in the basin have left less water available for irrigation in dry years and heightened tensions among farmers and other stakeholders including commercial fishermen, Native Americans, conservationists, hunters, anglers, and hydropower producers. This National Research Council report assesses two recent studies that evaluate various aspects of flows in the Klamath basin: (1) the Instream Flow Phase II study (IFS), conducted by Utah State University, and (2) the Natural Flow of the Upper Klamath Basin study (NFS), conducted by the U.S. Bureau of Reclamation (USBR). The report concludes that both studies offer important new information but do not provide enough information for detailed management of flows in the Klamath River, and it offers many suggestions for improving the studies. The report recommends that a comprehensive analysis of the many individual studies of the Klamath river basin be conducted so that a big picture perspective of the entire basin and research and management needs can emerge. Key Messages If these conclusions were borne out by studies incorporating experimental flows and monitored responses, managers would be able to have greater confidence that decisions to increase flows would have a beneficial effect on anadromous fishes in the lower river The Instream Flow Study Phase II did not include important water-quality attributes, such as dissolved oxygen levels, nutrient loadings, contaminants, and sediment concentrations, although each has important implications for the vitality of the fish populations of the Klamath River. The Natural Flow Study and the Instream Flow Study Phase II were major science and engineering investigations, but the linkage of one to the other was only partially achieved. The Natural Flow Study was seriously compromised by several fundamental issues, including its choice of a basic approach for understanding natural flows, choices of the models for calculations, and serious omissions of factors likely to influence river flows at the Iron Gate Dam gauge site. 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. The committee concluded that the Natural Flow Study includes calculated flows that are at best first approximations to useful estimates of such flows. The committee found important shortcomings in the Instream Flow Study Phase II and its use of various models and data. Two major shortcomings use of monthly data and lack of tributary analyses are so severe that that they should be addressed before decision makers can use the outputs of the study to establish precise flow regimes with confidence. The most important outcome of the Instream Flow Study was that it indicated that increases in existing flows downstream from Iron Gate Dam probably would benefit fish populations through improved physical habitat associated with more water and through reduced water temperatures. 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 When the science needs for the 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. current flow regime. These are improvements in flow because they include intra- and inter-annual variations and probably will enhance Chinook salmon growth and young-of-the-year production. is not possible to know how well the recommendations apply to any one species or to all the species as a whole. Indeed, most of the information was from Chinook salmon, which suggests that confidence in its applicability to that species would be greater than to other species. of the representativeness of the reaches used for detailed study, and the statistical approach to analyze the calculated set of instream flows did not use normalized data and did not have provisions for identifying serial autocorrelations.

Independent Panel Review of the Bay Delta Conservation Plan prepared for The Nature Conservancy and American Rivers

Nature Conservancy | September 19th, 2013

Two non-­governmental organizations, The Nature Conservancy (TNC) and American Rivers (AR), are evaluating their options for engagement with the Bay Delta Conservation P

Two non-­governmental organizations, The Nature Conservancy (TNC) and American Rivers (AR), are evaluating their options for engagement with the Bay Delta Conservation Plan (BDCP). If approved, the Plan would become a Habitat Conservation Plan (HCP) under the federal Endangered Species Act and a Natural Communities Conservation Plan (NCCP) under California law. The purpose of the Plan is to allow for construction of new water diversion facilities in the Sacramento-­San Joaquin Delta while also protecting aquatic and terrestrial species that may be adversely affected by the project and accompanying changes in the State Water Project (SWP) and Central Valley Project (CVP) operations. The Plan also includes habitat restoration and a commitment to assist in the conservation and recovery of species that are listed for protection under the federal and state Endangered Species Acts. With financial support from the S.D. Bechtel, Jr. Foundation, Saracino and Mount, LLC, convened an independent panel of experts, with technical support from NewFields, Inc., to evaluate portions of the Plan. The panel, working jointly with TNC and AR, developed a series of technical and legal questions about the Plan. This report provides answers to these questions, along with limited recommendations on how to improve BDCP. To simplify analysis, this review focuses on conditions for federally listed fishes during the Early Long Term (ELT), a decade after a permit would be issued (approximately year 2025). These are described in detail in the BDCP Effects Analysis and accompanying Environmental Impact Statement/Environmental Impact Report. We compared the performance of three different scenarios: a No Action Alternative (NAA) where no new North Delta diversion facility is constructed, a High Outflow Scenario (HOS) where the facilities are operated in a way that allows for occasional high spring and fall outflows, and a Low Outflow Scenario (LOS) with lower spring and fall outflows. The review also emphasizes in-­Delta and Sacramento River watershed conditions during the ELT, with less attention to San Joaquin River conditions and fishes. Although multiple data sources were used in this analysis, most hydrologic data came from CALSIM simulations conducted by BDCP consultants. The Panel strongly cautions about the conclusions drawn from these simulations. Flow simulations have three compounding uncertainties that can lead to significant error: (1) uncertainty in system understanding and future conditions, (2) model uncertainties (particularly the relationships between 1-­, 2-­, and 3-­dimensional models), and (3) behavioral/regulatory uncertainty where the models cannot capture the scope of human behavior in operating the projects under various conditions. These uncertainties, which are not described in BDCP documents well, makes all of our conclusions contingent on the projects actually being operated as simulated.

Independent Review Panel (IRP) Report for the 2014 Long-Term Operations Biological Opinions (LOBO) Annual Science Review

Delta Stewardship Council (Delta Council) | December 1st, 2014

Independent Review Panel (IRP) Report for the 2015 Long-Term Operations Biological Opinions (LOBO) Annual Science Review

Delta Stewardship Council (Delta Council) | December 1st, 2015

This report presents findings and opinions of the Independent Review Panel (IRP) assembled by the Delta Science Program to inform the National Marine Fisheries Service (N

This report presents findings and opinions of the Independent Review Panel (IRP) assembled by the Delta Science Program to inform the National Marine Fisheries Service (NMFS) and the U.S. Fish & Wildlife Service (USFWS) as to the efficacy of water operations and certain regulatory actions prescribed by their respective Long-term Operations Biological Opinions’ (LOBO) Reasonable and Prudent Alternative Actions (RPAs) as applied from October 1, 2014 through September 30, 2015 (Water Year 2015).  This year’s annual review focused primarily on: (1) Shasta Reservoir and Sacramento River temperature monitoring, modeling, and management, (2) the River Assessment for Forecasting Temperature (RAFT) decision support tool (model), (3) an Enhanced Particle Tracking Model (E-PTM), and (4) a USFWS report on past, present, and future approaches to incidental take of Delta Smelt.  After reviewing a required set of written documents (Appendix 1), the IRP convened at a public workshop in Sacramento, CA on 5-6 November 2015. The first day of the 2-day workshop included agency presentations and provided a forum for the IRP to interact and consider information presented on water operations, temperature modeling, monitoring and RPA Actions as implemented in yet another critically dry 2015 water year. On the second day, the IRP deliberated in a private session beginning at 9:00 a.m. in order to prepare and present their initial findings at the public workshop at 2:00 p.m., after which there was an opportunity for agency representatives, members of the public, and the IRP members to comment and otherwise exchange impressions and information. Subsequent IRP communication and deliberations were conducted via email and conference calls in the course of drafting this final report. Click here for federal agency response letter

Independent Review Panel (IRP) Report for the 2017 Long-term Operations Biological Opinions (LOBO) Biennial Science Review (January 24, 2018)

Delta Stewardship Council (Delta Council) | January 31st, 2018

Independent Review Panel Report for the 2016 California WaterFix Aquatic Science Peer Review

Delta Stewardship Council (Delta Council) | May 12th, 2016

This report presents the findings of the 2016 California WaterFix Aquatic Science Peer Review. An Independent Review Panel was convened by the Delta Science Program to pr

This report presents the findings of the 2016 California WaterFix Aquatic Science Peer Review. An Independent Review Panel was convened by the Delta Science Program to provide the National Marine Fisheries Service (NMFS), U.S. Fish and Wildlife Service (USFWS), and California Department of Fish and Wildlife (CDFW) with an independent scientific evaluation of the methods and approaches for developing the joint Biological Opinion requirements and analyses prepared for the CDFW 2081(b) Incidental Take Permit application for the California WaterFix. The Panel was charged with reviewing: (1) selected sections of the Biological Assessment (BA) that seeks to predict the effects of the WaterFix project on Endangered Species Act (ESA)-listed species and their designated critical habitats, (2) the draft Analytical Approach to developing the joint Biological Opinion (AABO) and (3) the proposed methods for assessing project effects on Longfin Smelt. After reviewing a set of documents (Appendix 1), the Panel participated in a public meeting in Sacramento, CA on April 5-6, 2016. On the first day of this meeting, the Panel interacted with agency representatives following their presentations on the three topics above. On day 2, the Panel communicated and discussed its preliminary findings to agency representatives and the public. This report summarizes the Panel’s findings and recommendations in full detail.

Instream flow evaluation: Temperature and passage assessment for salmonids in Mill Creek, Tehama County

California Department of Fish and Wildlife (CDFW) | May 8th, 2017

Mill Creek is among the essential streams for recovery and perpetuation of wild stocks of Central Valley spring-run Chinook salmon (Oncorhynchus tshawytscha), and support

Mill Creek is among the essential streams for recovery and perpetuation of wild stocks of Central Valley spring-run Chinook salmon (Oncorhynchus tshawytscha), and supports Central Valley steelhead trout (Oncorhynchus mykiss; Armentrout et al. 1998). In addition, Mill Creek is utilized by fall-run Chinook salmon, late fall-run Chinook salmon, and Pacific Lamprey (Entosphenus tridentatus). The Recovery Plan for Central Valley Chinook Salmon and Steelhead (NMFS 2014) classified Mill Creek as a high priority Core 1 watershed because of its potential to support independent viable populations. Mill Creek is also identified as a priority stream in the State Water Resources Control Board (SWRCB) Instream Flow Studies for the Protection of the Public Trust Resources: A Prioritized Schedule and Estimate of Cost (SWRCB 2010), and the US Fish and Wildlife Service (USFWS) Final Restoration Plan for the Anadromous Fish Restoration Program: A Plan to Increase Natural Production of Anadromous Fish in the Central Valley of California (USFWS 2001). The California Department of Fish and Wildlife (Department) has interest in ensuring that water flows within streams are maintained at levels which are adequate for long-term protection, maintenance, and proper stewardship of fish and wildlife resources. The Department’s Instream Flow Program develops scientific information to determine what flows are needed to maintain healthy conditions for fish and wildlife. For each species of interest, life stage, and stream, relationships between flow and habitat are developed. The Department recommends using the federal Instream Flow Incremental Methodology (IFIM) to evaluate and develop instream flow criteria for projects which may affect California’s aquatic resources. The IFIM process, and instream flow evaluations, in general, should include broad consideration of the structure and function of riverine systems while also providing examination of five core components (i.e., hydrology, biology, geomorphology, water quality, and connectivity) of the riverine system. The Public Resources Code (PRC) §10000-10005 outlines the Department’s responsibilities for developing and transmitting flow criteria to the SWRCB for consideration as set forth in 1257.5 of the Water Code. The results from this study are intended to be used, along with other supporting information and data, to identify stream flow requirements necessary for upstream passage of adult Chinook salmon and steelhead into the upper Mill Creek watershed pursuant to the Department’s PRC mandate. Flow criteria for lower Mill Creek will be developed by the Department in a future document.