Previous research combining data on the abundance of benthic invertebrates living in the northernmost section of the Barnegat Bay-Little Egg Harbor estuary with data on water quality suggested a community composition consistent with anthropogenic eutrophication. This part of the estuary, however, experiences both high-nutrient and low-salinity environmental conditions, which are both ecologically stressful to sensitive species and favorable to opportunistic species, complicating assessments of the direct effects of anthropogenic eutrophication. Here, geohistorical baselines were derived from molluscan death assemblages from four localities along a north-south gradient in the bay—two northern low-salinity, high-nutrient sites and two southern high-salinity, low-nutrient sites—to disentangle the effects of salinity and nutrient enrichment on the composition of benthic communities. Disturbance in the northern section of the estuary from freshwater input has been relatively consistent for thousands of years, but nutrient enrichment is a more recent stressor, developing only in the past few decades. The cause of the disturbed benthic community is unlikely to be anthropogenic eutrophication, if there is little discordance between the living and the death assemblage in the northern, low-salinity section of the bay. Comparisons of rank-order abundance (Spearman's rho) and taxonomic similarity (Jaccard-Chao index) of the living and death assemblages along the north-south gradient, however, indicate that compositional shifts occur at the northern sites only. A multivariate index analysis, M-AMBI, which integrates the AZTI Marine Biotic Index, a biotic index based on species sensitivity/tolerance to disturbances, with Shannon diversity and species richness, shows a similar pattern: ecological status shifts (from undisturbed to disturbed) in the northern but not southern sites along the north-south salinity gradient. These independent lines of evidence corroborate the inference that it is most likely anthropogenic eutrophication (and not salinity) disturbance driving observed patterns in benthic community composition. Further sampling and incorporation of geohistorical data into ongoing benthic monitoring in the estuary is recommended to establish ecological baselines where none exist, guide restoration planning, and assess the success of restoration efforts.