Boston Harbor is a natural urban harbor on the northeastern coast of the United States. The harbor’s watershed is home to more than one million people and has a long history of pollution. However, restoration efforts have greatly improved the harbor’s water quality over the past 50 years. The Massachusetts Water Resources Authority (MWRA) began building a new wastewater treatment plant for Greater Boston on Deer Island in the early 1990s. Starting in 1991, the MWRA began an annual benthic monitoring program within the harbor. Sediment samples are collected using a 0.04 square-meter van Veen grab sampler, fixed with buffered formalin, and washed through a 0.5 mm sieve. Living tissues are died with Rose Bengal and all macrofaunal individuals are picked and identified. For the sample years 2021 and 2022 the MWRA, provided the sediment samples, which contain shelly molluscan material. These samples containing the death assemblage were washed through 1 mm and 2 mm sieves. The 1-2 mm size fraction is not included in the present analysis. All bivalve sells retaining at least half the hinge were identified and enumerated. The 2021 and 2022 data were pooled by sampling station for both the living and death assemblages in order to increase sample sizes.

Analyses of the living and death assemblages show strong disagreement. Spearman’s rank-order correlation coefficients for all seven sampling stations are zero or negative while Chao’s similarity metric is less than 0.5 for six out of the seven stations. Pooling all 31 sampling years for the living data improves the rank-order correlation some, but does not change Chao’s similarity. Exploration of the life habits of the most abundant species in both assemblages show that the living assemblage has more deep-infaunal burrowers and surface deposit feeders while the death assemblage has more shallow-infaunal burrowers and suspension feeders. These results suggest that the molluscan fauna of Boston Harbor has undergone a major taxonomic and ecological shift. The precise causes of the changes are not yet known, but hypotheses include eutrophication from sewer effluent; increased sedimentation from deforestation and urban development; and industrial pollution. Unpublished results from silt deposition studies in the harbor and the loss of suspension feeders suggest increased siltation may be important.