Anthropogenic nutrient loading to coastal waters has increased producer biomass, leading to more frequent hypoxic events particularly in estuarine systems. To examine how eutrophication and hypoxia might alter consumer assemblages, we surveyed benthic communities in 2 subestuaries of Waquoit Bay, Massachusetts, representing a eutrophic-hypoxic regime and an oligotrophic-oxic regime. The number of consumer species and abundance of organisms were lower in the eutrophic estuary. In particular, there were fewer primary consumers, mainly small crustaceans. These differences in consumer community structure also alter trophic interactions. To examine changes in food web structure that might result from lower prey abundance, we sampled organisms from the 2 sub-estuaries and determined their trophic relationships based on nitrogen stable isotope ratios. Reduced numbers of primary consumers, and hence lower prey availability, led to changes in food web linkages. Specifically, omnivores shifted their diets from an omnivorous diet that is mainly carnivorous in the oligotrophic estuary to feeding mainly as herbivores in the eutrophic estuary, where prey were scarce and macroalgae were abundant. These shifts in trophic structure may have consequences for higher trophic levels.