Abstract
A zooplankton time series from the eastern Strait of Juan de Fuca in the Salish Sea was explored for its relationships to climate variability and survival of Puget Sound salmon populations. Vertical net tows were conducted ~ monthly over the upper 40 m from 2003 to 2018. Species with warm‐water associations that occur year‐round in Puget Sound, and species with cold‐water associations that dominate on the continental shelf during summer upwelling, were important members of the community at different times of year. Shifts in advection from Puget Sound and the coastal ocean were indicated by the abundance of Puget Sound‐dominant copepods Ditrichocorycaeus anglicus and Paracalanus spp. in summer through mid‐fall. In contrast, the coastal upwelling species Pseudocalanus mimus , Calanus marshallae , and Acartia longiremis were most abundant in fall through early spring, despite being the seasons they are least abundant on the continental shelf. Axis 1 of a Nonmetric Multidimensional Scaling ordination of the copepod community revealed clear seasonal cycles in community structure and longer‐term variance that correlated with the Pacific Decadal Oscillation and local temperatures. Axis 2 correlated to smolt‐to‐adult survival of Puget Sound coho salmon, but not with measured environmental factors. Copepod size composition and biogeographic affinities shifted along that axis. The mechanisms driving the shifts are not clear, but may indicate changes in trophic dynamics, or cryptic responses to environmental changes. These patterns suggest the importance of large‐scale climate influences and local environmental processes that affect estuarine circulation, population growth, and links to economically important fisheries.