Abstract Conductivity–temperature–depth (CTD), acoustic and net samples were taken through a series of passes in the eastern and central Aleutian Island archipelago to document regional differences in the physical and biological conditions. The water column in central passes had elevated salinity and depressed temperatures, indicating upwelling of deep water through the passes. The zooplankton community included the oceanic genera Neocalanus and Eucalanus, and the euphausiid Euphausia pacifica, all oceanic taxa. Eastern passes had significantly lower salinity and elevated temperature relative to the central passes, suggesting a more neritic environment. Calanus marshallae, Pseudocalanus, Acartia and Thysanoessa inermis, common neritic species, were observed in the eastern passes. Canonical correlation indicated that up to 50% of the observed variance in mean zooplankton abundance in the passes could be explained by salinity and temperature. Elevated sound scattering was observed in fronts and eddies in the passes, particularly at the northern ends of the passes, in association with elevated zooplankton abundance and biomass. The central passes were characterized as an oceanic environment, influenced primarily by Alaskan Stream water with its associated interzonal copepod species, while the eastern passes were influenced by the Alaska Coastal Current, which contains a mixture of oceanic and neritic zooplankton species.