California’s freshwater fishes: status and management

University of California, Davis (UC Davis) | January 31st, 2015

Fishes in Mediterranean climates are adapted to thrive in streams with dynamic environmental conditions such as strong seasonality in flows. However, anthropoge

Fishes in Mediterranean climates are adapted to thrive in streams with dynamic environmental conditions such as strong seasonality in flows. However, anthropogenic threats to species viability, in combination with climate change, can alter habitats beyond native species’ environmental tolerances and may result in extirpation. Although the effects of a Mediterranean climate on aquatic habitats in California have resulted in a diverse fish fauna, freshwater fishes are significantly threatened by alien species invasions, the presence of dams, and water withdrawals associated with agricultural and urban use. A long history of habitat degradation and dependence of salmonid taxa on hatchery supplementation are also contributing to the decline of fishes in the state. These threats are exacerbated by climate change, which is also reducing suitable habitats through increases in temperatures and changes to flow regimes. Approximately 80% of freshwater fishes are now facing extinction in the next 100 years, unless current trends are reversed by active conservation. Here, we review threats to California freshwater fishes and update a five-tiered approach to preserve aquatic biodiversity in California, with emphasis on fish species diversity. Central to the approach are man- agement actions that address conservation at different scales, from single taxon and species assemblages to Aquatic Diversity Management Areas, watersheds, and bioregions.

Changes in abundance and distribution of native and alien fishes of Suisun Marsh

American Fisheries Society (AFS) | July 29th, 1994

Overall fish abundance, abundance of introduced, native, and seasonal fish groups, and species diversity declined over a 14‐year period in Suisun Marsh, a portion of th

Overall fish abundance, abundance of introduced, native, and seasonal fish groups, and species diversity declined over a 14‐year period in Suisun Marsh, a portion of the San Francisco Bay estuary, and were associated with decreases in freshwater outflow and increases in salinity. Fish groups showed different patterns of abundance; large fluctuations in introduced and seasonal fish groups contrasted with a steady decline in native fish. Native species were found more often in small, dead‐end sloughs, seasonal species were found in larger sloughs, and introduced species were found in both habitats. Fish assemblage structure was less predictable than in an earlier (and shorter) study of the same community. Mixed groups of native and introduced species with similar freshwater and seasonal needs reflected effects of drought and increasing water diversions from the estuary. Chameleon goby Tridentiger trigonocephalus and yellowfin goby Acanthogobius flavimanus, two introduced species, fluctuated greatly in abundance in recent years, whereas other species declined steadily. Changes in fish abundance in the marsh reflect estuary‐wide changes and suggest that environmental disturbances coupled with introduced species are altering fish communities and hastening native fish declines.

Chinook salmon and green sturgeon migrate through San Francisco Estuary despite large distortions in the local magnetic field produced by bridges

PLOS | June 2nd, 2017

Empirical evidence exists that some marine animals perceive and orient to local distortions in the earth’s main static geomagnetic field. The magnetic fields produced b

Empirical evidence exists that some marine animals perceive and orient to local distortions in the earth’s main static geomagnetic field. The magnetic fields produced by undersea electric power cables that carry electricity from hydrokinetic energy sources to shore-based power stations may produce similar local distortions in the earth’s main field. Concerns exist that animals migrating along the continental shelves might orient to the magnetic field from the cables, and move either inshore or offshore away from their normal path. We have studied the effect of the Trans Bay Cable (TBC), an 85-km long, high voltage, direct current (DC) transmission line leading underwater from Pittsburg, CA to San Francisco, CA, on fishes migrating through the San Francisco Estuary. These included Chinook salmon smolts (Oncorhynchus tshawytscha) that migrate downstream through the San Francisco Estuary to the Pacific Ocean and adult green sturgeon (Acipenser medirostris), which migrate upstream from the ocean through the estuary to their spawning habitat in the upper Sacramento River and return to the ocean after spawning occurs. Based on a detailed gradiometer survey, we found that the distortions in the earth’s main field produced by bridges across the estuary were much greater than those from the Trans Bay Cable. The former anomalies exceeded the latter by an order of magnitude or more. Significant numbers of tagged Chinook salmon smolts migrated past bridges, which produced strong magnetic anomalies, to the Golden Gate Bridge, where they were recorded by dual arrays of acoustic tag-detecting monitors moored in lines across the mouth of the bay. In addition, adult green sturgeon successfully swam upstream and downstream through the estuary on the way to and from their spawning grounds. Hence, the large anomalies produced by the bridges do not appear to present a strong barrier to the natural seasonal movement patterns of salmonid smolts and adult green sturgeon.

Climate Change and the Delta

University of California, Davis (UC Davis) | October 1st, 2016

Climate change amounts to a fast approaching, “new” stressor in the Sacramento–San Joaquin Delta system. In response to California’s extreme natural hydroclimatic

Climate change amounts to a fast approaching, “new” stressor in the Sacramento–San Joaquin Delta system. In response to California’s extreme natural hydroclimatic variability, complex water-management systems have been developed, even as the Delta’s natural ecosystems have been largely devastated. Climate change is projected to challenge these management and ecological systems in different ways that are characterized by different levels of uncertainty. Future precipitation changes are less certain, with as many climate models projecting wetter conditions as drier. Warmer temperatures will likely enhance evaporation and raise water temperatures. Consequently, climate change is projected to yield both more extreme flood risks and greater drought risks. Effects on the Delta ecosystem that are traceable to warming include sea level rise, reduced snowpack, earlier snowmelt and larger storm-driven streamflow, warmer and longer summers, warmer summer water temperatures, and water-quality changes. These changes and their uncertainties will challenge the operations of water projects and uses throughout the Delta’s watershed and delivery areas. Although the effects of climate change on Delta ecosystems may be profound, the end results are difficult to predict, except that native species will fare worse than invaders. Successful preparation for the coming changes will require greater integration of monitoring, modeling, and decision-making across time, variables, and space than has been historically normal.

Climate change vulnerability of native and alien freshwater fishes of California: A systematic assessment approach

PLOS | May 22nd, 2013

Freshwater fishes are highly vulnerable to human-caused climate change. Because quantitative data on status and trends are unavailable for most fish species, a

Freshwater fishes are highly vulnerable to human-caused climate change. Because quantitative data on status and trends are unavailable for most fish species, a systematic assessment approach that incorporates expert knowledge was developed to determine status and future vulnerability to climate change of freshwater fishes in California, USA. The method uses expert knowledge, supported by literature reviews of status and biology of the fishes, to score ten metrics for both (1) current status of each species (baseline vulnerability to extinction) and (2) likely future impacts of climate change (vulnerability to extinction). Baseline and climate change vulnerability scores were derived for 121 native and 43 alien fish species. The two scores were highly correlated and were concordant among different scorers. Native species had both greater baseline and greater climate change vulnerability than did alien species. Fifty percent of California’s native fish fauna was assessed as having critical or high baseline vulnerability to extinction whereas all alien species were classified as being less or least vulnerable. For vulnerability to climate change, 82% of native species were classified as highly vulnerable, compared with only 19% for aliens. Predicted climate change effects on freshwater environments will dramatically change the fish fauna of California. Most native fishes will suffer population declines and become more restricted in their distributions; some will likely be driven to extinction. Fishes requiring cold water (,22uC) are particularly likely to go extinct. In contrast, most alien fishes will thrive, with some species increasing in abundance and range. However, a few alien species will likewise be negatively affected through loss of aquatic habitats during severe droughts and physiologically stressful conditions present in most waterways during summer. Our method has high utility for predicting vulnerability to climate change of diverse fish species. It should be useful for setting conservation priorities in many different regions.

Confirmation of Initial Incidental Take for Adult Delta Smelt for the 2018 Water Year

U.S. Fish and Wildlife Service (FWS) | January 4th, 2018

Considerations for Management of the Mouth State of California’s Bar-built Estuaries

Southern California Wetlands Recovery Project | January 10th, 2019

Bar-built estuaries are the dominant estuary type in California, and many of these small estuaries are subject to closure with a sand barrier separating a lagoon

Bar-built estuaries are the dominant estuary type in California, and many of these small estuaries are subject to closure with a sand barrier separating a lagoon estuary from the ocean for days, months or even years. In the lagoon impounded behind the sand barrier, water levels may rise or fall depending on net water budget and water quality extremes may develop. These conditions and the obstruction of fish passage motivate managed breaching of the sand barrier in many systems statewide – an intervention that alleviates or preempts environmental problems, but which also can result in undesirable secondary impacts due to the acute effect of a single breach or the chronic effect of repeated breaching over years. Management decisions are based on an implicit trade-off between anticipated benefits and costs that depend on the values and priorities of stakeholders. This report was written to provide an overview of considerations for managed breaching in California. It presents a synthesis of processes and phenomena related to mouth closure and breaching in general and uses this to identify potential impacts of breaching, without intending any judgment of which impacts are more or less desirable. Three specific systems are reviewed in detail: Los Peñasquitos Lagoon in San Diego County, Scott Creek Estuary in San Mateo County and Russian River Estuary in Sonoma County. While there are fundamental similarities in the closure and breaching cycle across all bar-built estuaries statewide, there is also an immense diversity between these systems due to differences in size, in hydrology (wet north to dry south), and in development (rural, urban, agricultural, road/rail). The local community is likely to develop the best management strategy where there is significant effort and experience in local monitoring, science, and stakeholder consultation. However, where there is limited monitoring, science or consultation, the considerations outlined in this report provide preliminary guidance – and comparison with one of the study systems can provide more specific insight to the potential impacts of breaching management decisions. We synthesize current understanding related to how mouth state influences estuary functions and conditions, which in turn affect ecological services. While both natural and managed breaching affect many processes and phenomena in the estuary, breaching events and managed breaching regimes do not occur in isolation and many other factors affect the estuary functions and conditions, including freshwater inputs, the adjacent landscape, and stressors in the watershed. However, managed breaching is one of very few short-term management options and therefore a valuable adaptive management tool, specifically in systems that are already perturbed or impacted by human encroachment. Although emergency breaches may be required in rare occasions, our recommendation is to develop a breaching strategy for specific systems in which breaching has been used or in which it is likely to be used as a management tool. In this context, we recommend ways in which science can provide improved support for management decisions and identify a few systems in California in which there is already a well-developed, science-based management plan. Associated document: "Wetlands on the Edge: The Future of Southern California's Wetlands - Regional Strategy 2018"

Critical Assessment of the Delta Smelt Population in the San Francisco Estuary, California

University of California, Davis (UC Davis) | July 1st, 2005

CVFPP Conservation Strategy Appendix G. Identification of Target Species and Focused Conservation Plans

California Department of Water Resources (DWR) | July 14th, 2016

 The purpose of the Conservation Strategy of the Central Valley Flood Protection Plan (CVFPP) is to provide direction for the California Department of Water Resources’

 The purpose of the Conservation Strategy of the Central Valley Flood Protection Plan (CVFPP) is to provide direction for the California Department of Water Resources’ (DWR’s) environmental stewardship activities related to integrated flood management in the Central Valley, and to provide a framework and support for programmatic permitting of flood management activities.  One goal of the Conservation Strategy is to contribute to the recovery and stability of native species populations and overall biotic community diversity. A set of potential target species was identified to support measurable objectives for this goal. For those target species with the greatest need for recovery of their populations, focused conservation planning was conducted. This appendix documents the process used for selecting the target species of the Conservation Strategy, including 17 target species for which focused conservation planning was conducted. The results of this focused planning are also provided in this appendix, in the form of focused conservation plans. This document is scheduled to be updated every 5 years.   Because the conservation needs of species change, in the future, additional species may become suitable targets for the Conservation Strategy. Therefore, during preparation of the 5-year updates to the CVFPP, the preliminary list of species in this appendix will be reevaluated using the same criteria described below. Species meeting these criteria will be added, and focused conservation plans will be developed for them and included in subsequent updates of the Conservation Strategy. During the public comment period, new information regarding the status of the delta smelt (Hypomesus transpacificus) and its habitat use in the Systemwide Planning Area (SPA) was made available, and a recovery plan for the species is expected to be released in 2016; therefore, this species will be considered for inclusion in the 2022 CVFPP and Conservation Strategy. Other species that were considered during the initial screening could be reconsidered, and targeted conservation plans may be developed. These species include the western pond turtle (Actinemys marmorata), tricolored blackbird (Agelaius tricolor), western red bat (Lasiurus blossevillii), and western burrowing owl (Athene cunicularia hypugaea). 

CVFPP Conservation Strategy Appendix H. Central Valley Chinook Salmon Rearing Habitat Required to Satisfy the Anadromous Fish Restoration Program Doubling Goal

California Department of Water Resources (DWR) | July 14th, 2016

NewFields and Cramer Fish Sciences, in collaboration with the California Department of Water Resources FloodSAFE Environmental Stewardship and Statewide Resources

NewFields and Cramer Fish Sciences, in collaboration with the California Department of Water Resources FloodSAFE Environmental Stewardship and Statewide Resources Office Conservation Strategy team, applied best available tools and data to estimate the area of suitable juvenile salmonid rearing habitat required in each of the Conservation Planning Areas (CPAs) to achieve the Anadromous Fish Restoration Program (AFRP) “doubling goal” for Chinook salmon populations. The AFRP goal was used to align the Conservation Strategy objectives with existing,longstanding efforts by partner resource management agencies. Historical and existing suitable rearing habitat area for juvenile salmonids was estimated with the Estimated Annual Habitat approach that uses measured hydrology and modeled hydraulic relationships between river flow and inundation area to calculate areas of inundation with timing, duration, and frequency suitable for juvenile California Chinook salmon rearing. The rearing habitat required to support the doubling goal populations was estimated using the Emigrating Salmonid Habitat Estimation model. The details of the approach and the full range of calculated results are presented in the following sections and appendices.