A sample design-based procedure for estimating pre-adult and adult delta smelt abundance is described. Using data from midwater trawl surveys taken during the months of September, October, November, and December for the years 1990 through 2006 and estimates of size selectivity of the gear from a covered codend experiment, stratified random sample ratio estimates of delta smelt abundance were made per month. The estimation procedure is arguably an improvement over the dimensionless delta smelt indices that have been used historically in that (1) the volume sampled is used in a manner that leads to directly interpretable numbers and (2) standard errors are easily calculated. The estimates are quite imprecise, i.e., coefficients of variation in the range of 100\% occurred. The point estimates are highly correlated with the monthly indices, and conclusions on abundance declines are quite similar. However, both the estimates and indices may suffer from selection biases if the trawl samples are not representative of the true densities. Future work is needed in at least three areas: (1) gathering additional information to determine the validity of assumptions made, in particular determining the possible degree of selection bias; (2) developing procedures that utilize survey data gathered from earlier life history stages, such as larval surveys; (3) embedding a life-history model into the population estimation procedure.

Long-term fish survey monitoring programs use a variety of fishing gears to catch fish, and the resulting catches are the basis for status and trends reports on the condition of different fish stocks. These catches can also be part of the data used to set stock assessment models, which establish harvest regulations, and to fit population dynamics models, which are used to analyze population viability. However, most fishing gears are size-selective, and fish size — among other possible covariates, such as environmental conditions — affects the probability that a fish will be caught in the path the gear sweeps. Failing to properly account for selectivity can adversely affect the ability to interpret and use status and trends measures, stock-assessment models, and population-dynamics models. Our side-by-side gear comparison study evaluated the selectivity of multiple open-water trawl surveys that have provided decades worth of information on the imperiled fish species Delta Smelt (Hypomesus transpacificus). We used data from the study to estimate gear selectivity curves for multiple trawls using two methods. The first method examines the total number of fish-at-length caught across all gears, and does not directly use or estimate fish length distribution in the population. The second method examines the total number of fish caught by each gear separately, and explicitly estimates fish length distribution in the population. The results from the two methods were similar, and we found that one trawl was highly efficient at catching larger Delta Smelt. This is the first formal multi-gear evaluation of how well survey gear used to monitor Delta Smelt in the San Francisco Estuary selects fish by size, and we plan to incorporate the results into Delta Smelt population models.

For nearly 50 years, the California Department of Fish and Wildlife has used a midwater trawl to intensively monitor fish populations in the San Francisco Estuary during the fall, sampling over 100 locations each month. The data collected have been useful for calculating indices of fish abundance and for detecting and documenting the decline of the endangered fish species delta smelt (Hypomesus transpacificus). However, efforts to calculate estimates of absolute abundance have been hampered by the lack of information on gear efficiency, in particular questions about contact selectivity and the effect of tow method on catches. To answer these questions we conducted a study that used a covered cod end on a net towed either near the surface, referred to as a surface tow, or throughout the water column, referred to as an oblique tow. A contact selectivity model was fit to estimate the probability that a delta smelt that has come into contact with the net is retained in the cod end of the net conditional on its body length. Full retention of delta smelt was found to occur around 60 mm fork length. Delta smelt catch densities for the surface tows were an order of magnitude greater than densities in the oblique tows, suggesting a surface orientation at the sub-adult life stage. These results represent an important step in being able to calculate absolute abundance estimates of the delta smelt population size using decades’ worth of monitoring data.

The decline of Sacramento River winter-run Chinook salmon (Oncorhynchus tshawytscha) remains one of the major water management issues in the Sacramento River. Few field studies have been published on winter-run, leaving gaps in our knowledge about their life history. This is especially true in the Sacramento–San Joaquin Delta, which provides essential rearing and migratory habitats for winter-run, and serves as the center of water operations for California. Using long-term monitoring data that identified winter-run-sized fish (“winter-run”) using length-at-date criteria, we examined patterns of juvenile migration in terms of geographic distribution, timing, numbers, and residence times. We analyzed the role of flow, turbidity, temperature, and adult escapement on the downstream movement (“migration”) of winter-run. Winter-run passed Knights Landing (rkm 144 or 51 rkm upstream of the Delta) between October and April, with substantial variation in peak time of entry that was strongly associated with the first high flows of the migration season. Specifically, the first day of flows of at least 400 m3 s-1 at Wilkins Slough (rkm 190) coincided with the first day that at least 5% of the annual total catch was observed at Knights Landing. While the period during which winter-run left the Delta spanned several months based on Chipps Island (rkm 29) catch data, the median catch typically occurred over a narrow window in March. Differences in timing of cumulative catch at Knights Landing and Chipps Island indicate that apparent residence time in the Delta ranges from 41 to 117 days, with longer apparent residence times for juveniles arriving earlier at Knights Landing. We discuss the potential importance of the Yolo Bypass floodplain as an alternative rearing and migratory corridor, contingent on the timing, duration, and magnitude of floodplain inundation. These results carry implications for habitat restoration and management of Sacramento River flows.