San Francisco Estuary and Watershed Science

We studied zooplankton distributions in the upper San Francisco Estuary at nested scales of tens to thousands of meters. The purposes of the study were to assess how well the Interagency Ecological Program (IEP) zooplankton monitoring represents abundance, and to investigate the variability of plankton on scales similar to those of foraging by fish. Samples were taken at three sites in the western Sacramento–San Joaquin Delta. We took 18 sets of six samples each with a plankton net along transects from near shore to center channel, and six sets of ten samples in the vicinity of a drifter either in mid-channel or near shore. Sampling took place in June–July 2014 during neap and spring tides, ebb and flood, day and night (transects only). Analysis focused on three common copepod species. Transect samples showed little consistent variation along transects, except that Pseudodiaptomus forbesi was less abundant nearshore than offshore by day at Big Break, the most landward site. The ratio of adults to adults + copepodites was strongly and positively related to turbidity by day but not by night, indicating demersal behavior. Drifter samples showed a minimum standard deviation of log10 sample counts of about 0.1, indicating that about two-thirds of replicate abundance values were within 80 % to 125% of the mean. A measure of difference between plankton samples at pairs of sample points was unrelated to distance between sample points for drifter samples, weakly related along transects for Limnoithona spp. stages, and strongly related for P. forbesi mainly because of the along-transect gradients at Big Break. The IEP sampling program is representative of plankton abundance except for demersal organisms, which can be ten-fold more abundant by night than by day. Small planktivorous fish could forage in patches of up to ~25% higher abundance than the mean.