Larvacean (=appendicularian) and pteropod (Limacina helicina) composition and abundance were studied with physical variables each May and late summer across 11 years (2001–2011), along a transect that crosses the continental shelf of the sub-Arctic Gulf of Alaska (GoA) and five stations within Prince William Sound (PWS). Collection with 53-µm plankton nets allowed the identification of larvaceans to species: five occurred in the study area. Temperature was the driving variable in determining larvacean community composition, yielding pronounced differences between spring and late summer, while individual species were also affected differentially by salinity and chlorophyll-a concentration. During the spring Oikopleura labradoriensis and Fritillaria borealis were most abundant, being present at all stations. Late summer had highest abundances of Oikopleura dioica at nearshore stations, while F. borealis dominated numerically at outer stations. The 53-µm plankton nets collected higher abundances of Oikopleura spp., Fritillaria spp. and L. helicina than coarser 150- and 505-µm plankton nets. Limacina helicina abundance had a significant interaction effect among years, seasons and station location. Limacina helicina abundance in nearby PWS explained 30% of the variability in pink salmon survival; however, no significant correlations existed with larvacean or L. helicina abundances from the GoA stations.