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.

Impact of Anthropogenic CO2 on the CaCO3 System in the Oceans

American Association for the Advancement of Science (AAAS) | July 16th, 2004

Rising atmospheric carbon dioxide (CO2) concentrations over the past two centuries have led to greater CO2 uptake by the oceans. This acidification process has changed

Rising atmospheric carbon dioxide (CO2) concentrations over the past two centuries have led to greater CO2 uptake by the oceans. This acidification process has changed the saturation state of the oceans with respect to calcium carbonate (CaCO3) particles. Here we estimate the in situ CaCO3 dissolution rates for the global oceans from total alkalinity and chlorofluorocarbon data, and we also discuss the future impacts of anthropogenic CO2 on CaCO3 shell–forming species. CaCO3 dissolution rates, ranging from 0.003 to 1.2 micromoles per kilogram per year, are observed beginning near the aragonite saturation horizon. The total water column CaCO3 dissolution rate for the global oceans is approximately 0.5  0.2 petagrams of CaCO 3-C per year, which is approximately 45 to 65% of the export production of CaCO 3.

Impacts of ocean acidification on marine organisms: quantifying sensitivities and interaction with warming

Wiley | February 21st, 2013

Ocean acidification represents a threat to marine species worldwide, and forecasting the ecological impacts of acidification is a high priority for science, management, a

Ocean acidification represents a threat to marine species worldwide, and forecasting the ecological impacts of acidification is a high priority for science, management, and policy. As research on the topic expands at an exponential rate, a comprehensive understanding of the variability in organisms' responses and corresponding levels of certainty is necessary to forecast the ecological effects. Here, we perform the most comprehensive meta‐analysis to date by synthesizing the results of 228 studies examining biological responses to ocean acidification. The results reveal decreased survival, calcification, growth, development and abundance in response to acidification when the broad range of marine organisms is pooled together. However, the magnitude of these responses varies among taxonomic groups, suggesting there is some predictable trait‐based variation in sensitivity, despite the investigation of approximately 100 new species in recent research. The results also reveal an enhanced sensitivity of mollusk larvae, but suggest that an enhanced sensitivity of early life history stages is not universal across all taxonomic groups. In addition, the variability in species' responses is enhanced when they are exposed to acidification in multi‐species assemblages, suggesting that it is important to consider indirect effects and exercise caution when forecasting abundance patterns from single‐species laboratory experiments. Furthermore, the results suggest that other factors, such as nutritional status or source population, could cause substantial variation in organisms' responses. Last, the results highlight a trend towards enhanced sensitivity to acidification when taxa are concurrently exposed to elevated seawater temperature.

Impacts of the California Drought from 2007 to 2009: Surprising Outcomes for California’s Agriculture, Energy, and Environment

Pacific Institute | June 16th, 2011

California’s three-year drought, which ended with this season’s cool and wet weather, had complicated and serious impacts that have been poorly understood and reporte

California’s three-year drought, which ended with this season’s cool and wet weather, had complicated and serious impacts that have been poorly understood and reported. Some of the impacts were expected; others were surprising. The Pacific Institute has just completed a nine-month assessment of new data from California’s agricultural, energy, and environmental sectors to evaluate actual consequences of the drought for the state. Analysis of state and federal data released over the past year finds that contrary to much of the media reporting, California’s agricultural community proved flexible and resilient, generating agri­cultural revenues in 2007, 2008, and 2009 that were the highest on record. And agriculture-related occupations remained a stable portion of total jobs available in areas directly impacted by water supply restrictions. Less frequently reported were the substantial impacts on energy production and aquatic ecosystems during the drought, which were economically and environmentally significant. “More severe drought is inevitable, and the U.S. – and California in particular – has not reformed drought monitoring, evaluation, planning, and response strategies the way other countries and regions have,” said Juliet Christian-Smith, senior research associate at the Pacific Institute and lead author of the report. “To become more resilient to future droughts, it will be critical to shift from crisis-driven responses to long-term mitigation strategies.” The Pacific Institute analysis, Impacts of the California Drought from 2007-2009, focused on three drought-sensitive sectors: agricultural production, energy production, and ecosystem health.  

Inclusion of Pesticide Transformation Products Is Key to Estimating Pesticide Exposures and Effects in Small U.S. Streams

American Chemical Society (ACS) | March 10th, 2021

Improved analytical methods can quantify hundreds of pesticide transformation products (TPs), but understanding of TP occurrence and potential toxicity in aquatic ecosyst

Improved analytical methods can quantify hundreds of pesticide transformation products (TPs), but understanding of TP occurrence and potential toxicity in aquatic ecosystems remains limited. We quantified 108 parent pesticides and 116 TPs in more than 3 700 samples from 442 small streams in mostly urban basins across five major regions of the United States. TPs were detected nearly as frequently as parents (90 and 95% of streams, respectively); 102 TPs were detected at least once and 28 were detected in >20% samples in at least one region—TPs of 9 herbicides, 2 fungicides (chlorothalonil and thiophanate-methyl), and 1 insecticide (fipronil) were the most frequently detected. TPs occurred commonly during baseflow conditions, indicating chronic environmental TP exposures to aquatic organisms and the likely importance of groundwater as a TP source. Hazard quotients based on acute aquatic-life benchmarks for invertebrates and nonvascular plants and vertebrate-centric molecular endpoints (sublethal effects) quantify the range of the potential contribution of TPs to environmental risk and highlight several TP exposure–response data gaps. A precautionary approach using equimolar substitution of parent benchmarks or endpoints for missing TP benchmarks indicates that potential aquatic effects of pesticide TPs could be underestimated by an order of magnitude or more.

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 Report for the 2016-2017 California WaterFix Aquatic Science Peer Review Phase 2B

Delta Stewardship Council (Delta Council) | March 7th, 2017

This report presents the findings of the 2016 California WaterFix (CWF) Aquatic Science Peer Review, Phase 2B. An Independent Review Panel (Panel; Appendix 1) was convene

This report presents the findings of the 2016 California WaterFix (CWF) Aquatic Science Peer Review, Phase 2B. An Independent Review Panel (Panel; Appendix 1) was convened by select staff of the Delta Science Program to provide the National Marine Fisheries Service (NMFS), U.S. Fish and Wildlife Service (FWS), and California Department of Fish and Wildlife (CDFW) with the views of experts not involved in the CWF Endangered Species Act (ESA) consultation and 2081(b) permit on the use of best available scientific information in the California WaterFix Incidental Take Permit (CWF ITP) application.  The agencies further requested review of the Adaptive Management Framework proposed to integrate future scientific research, monitoring, and decision making during construction and operations of CWF. Accordingly, the Panel was charged with reviewing NMFS’ analytical approach and FWS’ analytical framework, status of the species and critical habitat, environmental baseline, and effects analysis sections of the draft BiOps on CWF for all ESA- and California ESA (CESA)-listed aquatic species and their critical habitat (see Charge, Appendix 2). After reviewing the charge and a set of prescribed documents (Appendix 3), the Panel participated in a public meeting in Sacramento, CA on January 23-24, 2017. On the first day of this meeting, the Panel interacted with agency representatives after they gave presentations on the topics above. On the second day, the Panel communicated internally and then discussed its preliminary findings with agency representatives and the public (Appendix 4).

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.