Understanding the causes of and quantifying the impacts of ecosystem shifts over time in marine and estuarine environments are critical to the effective management of coastal resources. Fishes are a crucial resource, and the abundance and diversity of species can indicate the productivity and health of an environment. Two series of juvenile fish surveys separated by 50 years were conducted along Barnegat Bay, New Jersey, to compare the historical composition and abundance of the Bay's fish species to those of the present day. Two sites were sampled by beach seine in both series and assessed for changes in species abundance, diversity, and composition over time. Differences in physical parameters (temperature, salinity) and habitat characteristics between the surveys were characterized. Principal component analysis indicated changes in the community structure of one of the two sites from its historical state, driven by significant shifts in the abundance of several key species. A shift in the ranks of species common to both datasets was documented at both sites, as was the loss of northern-associated species and introduction of southern-associated species. Change in habitats from seagrass beds and natural shorelines to sandy, unvegetated environments, combined with increases in temperature and salinity, was identified as drivers of the shifts in species between the datasets. Continued loss of habitat and environmental changes could further exacerbate the declines in important taxa already seen across 50 years of climate change and urbanization of this significant estuary.