We collected suspended particulate matter (seston) and zooplankton samples from Lake Washington in Seattle, Washington, U.S.A., over a 10-month period to investigate the effects of food availability on zooplankton fatty acid (FA) composition. The percentage of nutritionally critical omega3 polyunsaturated fatty acids (PUFA) in the seston varied from 8% of the FA pool in midsummer to 30% during the spring diatom bloom. Zooplankton accumulated much higher percentages omega3 PUFA than was available in the seston. In particular, cladocerans preferentially accumulated eicosapentaenoic acid (EPA, 20:5omega3), copepods accumulated docosahexaenoic acid (DHA, 22:6omega3), and both copepods and cladocerans accumulated 18 carbon chain omega3 PUFAs (C18 omega3). By comparison, the FA of zooplanktivorous juvenile sockeye salmon (Oncorhynchus nerka) were strongly dominated by EPA (12.5% +/- 2.1%) and DHA (28.2% +/- 8.7%). The saturated fatty acid and the arachidonic acid (ARA, 20:4omega6) composition of Diaptomus ashlandi was strongly (r2 = 0.76) and moderately (r2 = 0.54) correlated with the prevalence of these FAs in the seston. Furthermore, the DHA content of Diaptomus was moderately correlated with the seston's DHA content (r2 = 0.45) and very strongly correlated with seston EPA (r2 = 0.89). Since EPA was the most prevalent PUFA in the seston and DHA was the most prevalent PUFA in Diaptomus, these results suggest that Diaptomus may synthesize DHA from the EPA in their food. In general, zooplankton species in Lake Washington were strongly enriched with those FA molecules that are most physiologically important for fish nutrition (i.e., ARA, EPA, and DHA), indicating a clear mechanism by which changes in seston composition influence fisheries ecology.