Abstract Associations between cetacean distributions, oceanographic features, and bioacoustic backscatter were examined during two process cruises in the northern California Current System (CCS) during late spring and summer 2000. Line-transect surveys of cetaceans were conducted across the shelf and slope, out to 150 km offshore from Newport, Oregon (44.6°N) to Crescent City, California (41.9°N), in conjunction with multidisciplinary mesoscale and fine-scale surveys of ocean and ecosystem structure. Occurrence patterns (presence/absence) of cetaceans were compared with hydrographic and ecological variables (e.g., sea surface salinity, sea surface temperature, thermocline depth, halocline depth, chlorophyll maximum, distance to the center of the equatorward jet, distance to the shoreward edge of the upwelling front, and acoustic backscatter at 38, 120, 200 and 420 kHz) derived from a towed, undulating array and a bioacoustic system. Using a multiple logistic regression model, 60.2% and 94.4% of the variation in occurrence patterns of humpback whales Megaptera novaeangliae during late spring and summer, respectively, were explained. Sea surface temperature, depth, and distance to the alongshore upwelling front were the most important environmental variables during June, when humpbacks occurred over the slope (200–2000 m). During August, when humpbacks concentrated over a submarine bank (Heceta Bank) and off Cape Blanco, sea surface salinity was the most important variable, followed by latitude and depth. Humpbacks did not occur in the lowest salinity water of the Columbia River plume. For harbor porpoise Phocoena phocoena, the model explained 79.2% and 70.1% of the variation in their occurrence patterns during June and August, respectively. During spring, latitude, sea surface salinity, and thermocline gradient were the most important predictors. During summer, latitude and distance to the inshore edge of the upwelling front were the most important variables. Typically a coastal species, harbor porpoises extended their distribution farther offshore at Heceta Bank and at Cape Blanco, where they were associated with the higher chlorophyll concentrations in these regions. Pacific white-sided dolphin Lagenorhynchus obliquidens was the most numerous small cetacean in early June, but was rare during August. The model explained 44.5% of the variation in their occurrence pattern, which was best described by distance to the upwelling front and acoustic backscatter at 38 kHz. The model of the occurrence pattern of Dall's porpoise Phocoenoides dalli was more successful when mesoscale variability in the CCS was higher during summer. Thus, the responses of cetaceans to biophysical features and upwelling processes in the northern CCS were both seasonally and spatially specific. Heceta Bank and associated flow-topography interactions were very important to a cascade of trophic dynamics that ultimately influenced the distribution of foraging cetaceans. The higher productivity associated with upwelling near Cape Blanco also had a strong influence on the distribution of cetaceans.