Estuaries provide critical habitat for food webs supporting fish and shellfish consumed by humans, but estuarine ecosystem health has been threatened by increases in nitrogen loading as well as inputs of the neurotoxin, mercury (Hg), which biomagnifies in food webs and poses risk to humans and wildlife. In this study, the effects of nutrient loading on the fate of Hg in shallow coastal estuaries were examined to evaluate if their interaction enhances or reduces Hg bioavailability in sediments, the water column, and concentrations in lower trophic level fish (Fundulus heteroclitus and Menidia menidia). Multiple sites were sampled within two human impacted coastal lagoons, Great South Bay (GSB) and Jamaica Bay (JB), on the southern coast of Long Island, NY, United States of America (U.S.A.). Carbon (C), nitrogen (N), sulfur (S), Hg, and methylmercury (MeHg) were measured in surface sediments and the water column, and total Hg (THg) was measured in two species of forage fish. Minimal differences were found in dissolved and particulate Hg, dissolved organic carbon (DOC), and salinity between the two bays. Across lagoons, concentrations of chlorophyll-a were correlated with total suspended solids (TSS), and water column THg and MeHg was largely associated with the particulate fraction. Methylmercury concentrations in particulates decreased with increasing TSS and chlorophyll-a, evidence of biomass dilution of MeHg with increasing productivity at the base of the food chain. Water column Hg was associated with THg concentrations in Atlantic silversides, while mummichog THg concentrations were related to sediment concentrations, reflecting their different feeding strategies. Finally, higher nutrient loading (lower C:N in sediments) while related to lower particulate concentrations coincided with higher bioaccumulation factors (BAF) for Hg in both fish species. Thus, in shallow coastal lagoons, increased nutrient loading resulted in decreased Hg concentrations at the base of the food web but resulted in greater bioaccumulation of Hg to fish relative to its availability in algal food.