We have been investigating microbial communities in sediments from New Bedford Harbor (NBH), Massachusetts, USA, for a number of years. NBH is a U.S. Environmental Protection Agency-designated Superfund site heavily contaminated with polychlorinated biphenyls, polycyclic aromatic hydrocarbons, and heavy metals. Microorganisms are thought to contribute to the fate and distribution of contaminants in NBH through a variety of mechanisms, including direct transformations and formation of soluble and insoluble species. Our more recent research has focused on changes in microbial community structure and function in response to exposure to toxic contaminants, with the ultimate goal of using microbes as ecotoxicological tools. Microbial diversity, as measured by restriction fragment-length polymorphism analysis, changes along pollution gradients, with an apparent increase in diversity at the most contaminated sites, concomitant with an increase in genetic relatedness. Current work on microbial communities examines the presence of arsenic-resistance genes in NBH isolates. In collaboration with the Plymouth Environmental Research Center, Plymouth University, United Kingdom, we have also used more conventional ecotoxicological approaches to examine the health of the NBH biota.