Hydrodynamics and habitat interact to structure fish communities within terminal channels of a tidal freshwater delta

Ecological Society of America (Wiley) | January 13th, 2023

Terminal channels were historically a common feature of tidal delta ecosystems but have become increasingly rare as landscapes have been modified. Tidal hydrodynamics are

Terminal channels were historically a common feature of tidal delta ecosystems but have become increasingly rare as landscapes have been modified. Tidal hydrodynamics are a defining feature in tidal terminal channel ecosystems from which native aquatic communities have evolved. However, few studies have explored the relationship between fish community structure and hydrodynamics in these tidal terminal channel ecosystems. We sampled fish communities throughout a network of terminal channels within the northeasternmost region of the San Francisco Estuary to determine the relationship between fish community structure and hydrodynamics within these environments. We collected two years (2017 and 2018) of fish community samples using gill nets and analyzed data using multivariate community analyses and count models. We found metrics of fish diversity and counts of native fishes to be greatest upstream (farthest from tidal influence) of the tidal excursion within terminal channels. Counts of non-native fishes were less affected by this hydrodynamic feature of terminal channels and more tightly correlated to local habitat conditions (e.g., water temperature, depth). Our results suggest that channel hydrodynamics plays a role in structuring fish communities within terminal channels, particularly native fishes. These results indicate that hydrodynamics in tidal delta ecosystems may be able to be altered in ways that benefit native fishes without the cost of water pumping.

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

Initial Alternatives Information Report for the North/Central Delta Improvement Study (Delta Cross Channel, Franks Tract, and Through- Delta Facility Evaluation)

U.S. Bureau of Reclamation (USBR) | March 17th, 2010

The U.S. Department of the Interior (Interior) Bureau of Reclamation (Reclamation) and the California Department of Water Resources (DWR) are evaluating the feasibility o

The U.S. Department of the Interior (Interior) Bureau of Reclamation (Reclamation) and the California Department of Water Resources (DWR) are evaluating the feasibility of using conveyance and operations actions in the north and central region of the Sacramento–San Joaquin River Delta (Delta) to improve water quality and fish conditions. Specifically, Reclamation is evaluating the feasibility of these actions in the North/Central Delta Improvement Study (NoCDIS or Study). The Initial Alternatives Information Report (IAIR) identifies, discusses, and screens measures to address the problems and opportunities. These measures are used to develop initial alternatives. Initial alternatives from the IAIR will be incorporated into and refined in the subsequent Plan Formulation Report (PFR). Subject to continued appropriations and a determination of federal interest, the Study should culminate in an Environmental Impact Statement/Environmental Impact Report (EIS/EIR) and a Feasibility Report. Reclamation is the federal lead agency for National Environmental Policy Act (NEPA) compliance, and DWR is the state lead agency for California Environmental Quality Act (CEQA) compliance.

Inter-population differences in salinity tolerance of adult wild Sacramento splittail: osmoregulatory and metabolic responses to salinity

Conservation Physiology (Society of Experimental Biology) | December 10th, 2020

The Sacramento splittail (Pogonichthys macrolepidotus) is composed of two genetically distinct populations endemic to the San Francisco Estuary (SFE). The allop

The Sacramento splittail (Pogonichthys macrolepidotus) is composed of two genetically distinct populations endemic to the San Francisco Estuary (SFE). The allopatric upstream spawning habitat of the Central Valley (CV) population connects with the sympatric rearing grounds via relatively low salinity waters, whereas the San Pablo (SP) population must pass through the relatively high-salinity Upper SFE to reach its allopatric downstream spawning habitat. We hypothesize that if migration through SFE salinities to SP spawning grounds is more challenging for adult CV than SP splittail, then salinity tolerance, osmoregulatory capacity, and metabolic responses to salinity will differ between populations. Osmoregulatory disturbances, assessed by measuring plasma osmolality and ions, muscle moisture and Na+-K+-ATPase activity after 168 to 336 h at 11 salinity, showed evidence for a more robust osmoregulatory capacity in adult SP relative to CV splittail. While both resting and maximum metabolic rates were elevated in SP splittail in response to increased salinity, CV splittail metabolic rates were unaffected by salinity. Further, the calculated difference between resting and maximum metabolic values, aerobic scope, did not differ significantly between populations. Therefore, improved osmoregulation came at a metabolic cost for SP splittail but was not associated with negative impacts on scope for aerobic metabolism. These results suggest that SP splittail may be physiologically adjusted to allow for migration through higher-salinity waters. The trends in interpopulation variation in osmoregulatory and metabolic responses to salinity exposures support our hypothesis of greater salinity-related challenges to adult CV than SP splittail migration and are consistent with our previous findings for juvenile splittail populations, further supporting our recommendation of population-specific management.

Interagency Fish Passage Steering Committee 2014 Annual Report Focusing on the Shasta Dam Fish Passage Evaluation

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