In California's Sacramento-San Joaquin estuary, environmental protection and habitat restoration efforts directed at a threatened native osmerid, the delta smelt (Hypomesus transpacificus), are complicated by the presence of a morphologically similar non-native congener, the wakasagi (H. nipponensis), transported to the estuary from upstream reservoirs. In order to better define delta smelt critical habitat and to evaluate the potential for habitat overlap by these two species, we compared the tolerances of the two species to temperature, salinity, and water velocity, environmental factors that vary spatially and temporally within the estuary. For fishes acclimated to 17°C and fresh water (0 ppt), we measured critical thermal maxima and minima, chronic upper salinity tolerance limits, and critical swimming velocities. Wakasagi had higher critical thermal maxima (29.1°C vs. 25.4°C for delta smelt), lower critical thermal minima (2.3°C vs. 7.5°C for delta smelt), higher upper salinity tolerances (26.8 ppt vs. 19.1 ppt for delta smelt), and swam faster (for 6-6.9 cm SL fish, 43.3 cm s vs. 28.2 cm s for delta smelt) than delta smelt. This suggests that the wide seasonal and year-to-year fluctuations in temperature, salinity, and flow typical in the estuary would not exclude wakasagi, although their eggs and larvae may be less tolerant. With respect to these factors, the native delta smelt may be at a physiological disadvantage, particularly in habitats with suboptimal environmental conditions, and may be excluded from shallow-water habitat restoration sites, which are characterized by poor circulation, low flows, and more environmentally extreme conditions. The low abundance of wakasagi in the estuary recorded to date may indicate that factors other than temperature, salinity, and flow determine wakasagi distribution.

Protected evolutionarily significant units (ESUs) of salmonids require objective and measurable criteria for guiding their recovery. In this report, we develop a method for assessing population viability and two ways to integrate these population-level assessments into an assessment of ESU viability. Population viability is assessed with quantitative extinction models or criteria relating to population size, population growth rate, the occurrence of catastrophic declines, and the degree of hatchery influence. ESU viability is assessed by examining the number and distribution of viable populations across the landscape and their proximity to sources of catastrophic disturbance. Central Valley spring-run and winter-run Chinook salmon ESUs are not currently viable, according to the criteria-based assessment. In both ESUs, extant populations may be at low risk of extinction, but these populations represent a small portion of the historical ESUs, and are vulnerable to catastrophic disturbance. The winter-run Chinook salmon ESU, in the extreme case, is represented by a single population that spawns outside of its historical spawning range. We are unable to assess the status of the Central Valley

We used a large, annular flume equipped with a simulated fish screen to assess the swimming and behavioral responses of juvenile Chinook salmon Oncorhynchus tshawytscha to two‐vector flows typifying habitats near water diversions, where small fish may become entrained. Groups of 20 fish (4.4–7.9 cm long, at 12°C or 19°C) were tested for 2 h at one of nine experimental flow regimes derived from combinations of three (approach) velocities perpendicular to the screen and three (sweeping) velocities parallel to the screen and a (0‐cm/s) control during daytime (lighted) and nighttime (dark) conditions. In the high‐velocity (resultant vector) flow regimes, all fish swam at velocities comparable to the critical swimming velocities measured for similar‐sized conspecifics, suggesting that exposure to such flow conditions near a water diversion is energetically expensive. Although most fish exhibited strong positive rheotaxis, older (smolt‐size) fish acclimated to the warmer temperature exhibited higher rates of negative rheotaxis (particularly in the intermediate‐velocity flow regimes), a behavior consistent with downstream migration. Fish life stage (length), time of day (light level), and water velocity influenced swimming velocity; sweeping velocity, swimming velocity, and rheotaxis influenced screen passage velocity. Regardless of the flow regime, juvenile Chinook salmon contacted the screen most frequently at night, and nighttime contact rates were not affected by the velocity of either flow vector. During the daytime, screen contact rates were inversely related to sweeping velocity and independent of approach velocity. Injury rates were low and unrelated to either flow or screen contact rates, and survival rates were high (>99%) in these predator‐free experiments. Fish screen designs that minimize screen exposure duration (e.g., via reduced screen length or increased sweeping velocities) should optimally protect valuable juvenile Chinook salmon, a species that encounters multiple water diversions along many of its migratory paths to the ocean.

Effective conservation and recovery planning for Central Valley steelhead requires an understanding of historical population structure. We describe the historical structure of the Central Valley steelhead evolutionarily significant unit using a multi-phase modeling approach. In the first phase, we identify stream reaches possibly suitable for steelhead spawning and rearing using a habitat model based on environmental envelopes (stream discharge, gradient, and temperature) that takes a digital elevation model and climate data as inputs. We identified 151 patches of potentially suitable habitat with more than 10 km of stream habitat, with a total of 25,500 km of suitable habitat. We then measured the distances among habitat patches, and clustered together patches within 35 km of each other into 81 distinct habitat patches. Groups of fish using these 81 patches are hypothesized to be (or to have been) independent populations for recovery planning purposes. Consideration of climate and elevation differences among the 81 habitat areas suggests that there are at least four major subdivisions within the Central Valley steelhead ESU that correspond to geographic regions defined by the Sacramento River basin, Suisun Bay area tributaries, San Joaquin tributaries draining the Sierra Nevada, and lower-elevation streams draining to the Buena Vista and Tulare basins, upstream of the San Joaquin River. Of these, it appears that the Sacramento River basin was the main source of steelhead production. Presently, impassable dams block access to 80% of historically available habitat, and block access to all historical spawning habitat for about 38% of the historical populations of steelhead.

Protection of endangered species that are restricted to highly modified ecosystems and threatened by anthropogenic activities often includes regulatory design and operational criteria for structures and facilities located within the species' critical habitat. In many freshwater systems, loss of fishes at water diversions has contributed to population declines of multiple species. Fish screens prevent removal of fish from the habitat; however, under current design criteria, the degree of protection provided by screens is unknown for most affected species. We used a large laboratorybased flume to observe and quantify the responses of delta smelt Hypomesus transpacificus, an endangered osmerid threatened by water diversions in California's Sacramento-San Joaquin Estuary, to a simulated fish screen. For a range of flow and environmental conditions, we measured screen contact frequency, swimming behavior, injuries, and survival. Delta smelt experienced frequent temporary contact with the screen, and contact rates were influenced by flow and time of day-light level. Contact was injurious, and postexperiment mortality rates were directly related to both contact frequency and severity as well as temperature. Quantitative models showed that, for this species, both behavioral responses such as swimming velocity and physiological responses to fish screen contact, as modified by environmental conditions, controlled the species' performance and its risk from the diversion and the screen. The results illustrate that ecologically effective protection strategies and regulatory criteria developed on the basis of multiple integrated responses of the organism to the stressor offer greater benefits and certainty to both the organism and the regulated activities.