Abstract Radiolaria, as other plankton, appear to be highly tuned to specific oceanographic environments. Thus, in a transitional region such as the eastern North Pacific, where many different water masses are mixed, radiolaria provide very sensitive tracers of these water masses and the currents that carry them. We present the first two years of radiolarian results from the Multitracers sediment trap study across the northern California Current System. Three moorings, positioned along a transect at approximately 130, 280 and 650 km from the coast, sample a wide variety of oceanographic conditions both spatially and temporally. Selected species or species groups are presented along with hydrographic data from the region in order to demonstrate the basic trends in the radiolarian data and illustrate their relationships to fluctuations in their physical environment. Multiple linear regression is used to explore the relationship between radiolarian composition and the export of carbon from this system. The most important physical process controlling variability in the radiolarian composition along this transect is attributed to variability in the intensity of the southward-flowing California Current. The seasonality of the California Current is clearly reflected by changes in the composition of the radiolarian trap assemblages; very different species dominate this region in summer as compared to winter. In addition to seasonal trends, evidence in both the offshore and onshore environments suggests significant differences between years. This region appears to have been more strongly influenced by cold, subarctic water during the winter of 1988/1989 than during the previous year. The relationship between radiolarian species abundances and the flux of organic carbon strongly indicates that a number of different oceanographic processes contribute to enhanced productivity at these sites. This has important implications when making inferences from the geological record about past changes in the intensity of upwelling in this eastern boundary current system.