Eutrophication forces shifts in estuarine producer assemblages from seagrass meadows to communities dominated by macroalgae. This restructuring of the benthic producer assemblage presents challenges and alters food resources available to consumers. We examined food web relationships in 3 sub-estuaries of the Waquoit Bay system, Massachusetts, USA, that span a gradient of relatively low nitrogen loads of 5, 10, and 34 kg N ha-1 yr-1. We detected effects on benthic macrophytes across this range of N loads with reduced seagrass cover and higher macroalgal biomass as N loading increased. The difference in N loading to these estuaries could also be detected in δ15N signatures of the benthic community. Producers and consumers were enriched in δ15N in response to increasing N load and incorporation of isotopically heavy nitrogen from wastewater sources. The differences in the relative availability of seagrass and macroalgae associated with the N load gradient were reflected in consumer diets. δ13C of producers were similar among the estuaries, but for consumers the isotopic signatures differed, suggesting they did not feed on the same primary producer sources. Using IsoSource, we modeled the diets of 2 herbivores, the amphipod Cymadusa compta and the isopod Erichsonella filiformis. At the lower N loads, more seagrass and detritus were consumed, whereas at the high N load where macroalgae was the dominant vegetation type, algae dominated the diet. The resulting C isotopic signatures appear to have permeated to higher trophic levels, suggesting C flow through the system differs across the range of N loads sampled. In the most pristine estuary, the overall food web was supported mainly by seagrass, its epiphytes and detritus, but macroalgal C was more important where this was the dominant type of macrophyte. These results demonstrate that C pathways through coastal food webs may be altered at earlier stages of eutrophication than previous studies have suggested.