Cobscook Bay is an 11- km2 geographically complex, boreal, and macrotidal bay in eastern Maine. The physical environment, primary producers, and invertebrate assemblage of the bay are well-characterized, but no contemporary data exist on its finfish assemblage. We sampled the finfish assemblage of Cobscook Bay from 2011 to 2013 in May, June, August, and September to create a baseline dataset suitable for future comparisons. We also examined the composition, diversity, and annual changes in the assemblage. We sampled in the subtidal and intertidal zones using seines (n = 390), fyke nets (n = 72), and benthic (n = 112) and pelagic (n = 111) trawls; sampling was divided among the bay's 3 different sub-bays. We collected more than 60,000 individuals from 46 species. We employed species richness, Simpson's index of diversity, and non-metric multidimensional scaling (with the Bray—Curtis and Horn—Morisita indices) to examine spatial and temporal variation of finfish assemblages throughout the bay. Our analysis suggested that data collected in the subtidal pelagic were not a representative sample of that assemblage. Therefore, we considered 2 assemblages: the intertidal and subtidal benthic. Assemblage composition and species' relative abundances were different at diel, monthly, and annual timescales and were associated with changes in the catch rate of ubiquitous species. In the intertidal, these species included Gasterosteus aculeatus (Threespine Stickleback), Clupea harengus (Atlantic Herring), Alosa pseudoharengus (Alewife), and Menidia menidia (Atlantic Silverside). In the subtidal, the common species were Atlantic Herring and Pseudopleuronectes americanus (Winter Flounder). Statistical analyses indicated that both spatial and temporal factors were significant predictors of assemblage evenness. The sampling design, albeit complex, was sufficient to capture these differences and characterize these assemblages. Implications for future studies are that the study design must be sufficiently complex to capture the anticipated spatial and temporal variability inherent in such dynamic environments. Furthermore, given recent warming trends in the Gulf of Maine, this study's results suggest the importance of thoroughly understanding local temporal and ecosystem variability.