We measured mercury (Hg) isotope ratios in sediments and various estuarine organisms (green crab, blue mussel, killifish, eider) to investigate methylmercury (MMHg) sources and exposure pathways in five Northeast coast (U.S.) estuaries. The mass independent Hg isotopic compositions (MIF; Δ¹⁹⁹Hg) of the sediments were linearly correlated with the sediment 1/Hg concentrations (Δ¹⁹⁹Hg: r² = 0.77, p < 0.05), but the mass dependent isotope compositions (MDF; δ²⁰²Hg) were not (r² = 0.26, p = 0.16), reflecting inputs of anthropogenic Hg sources with varying δ²⁰²Hg. The estuarine organisms all display positive Δ¹⁹⁹Hg values (0.21 to 0.98 ‰) indicating that MMHg is photodegraded to varying degrees (5–12%) prior to entry into the food web. The δ²⁰²Hg and Δ¹⁹⁹Hg values of most organisms can be explained by a mixture of MMHg and inorganic Hg from sediments. At one contaminated site mussels have anomalously high δ²⁰²Hg, indicating exposure to a second pool of MMHg, compared to sediment, crabs and fish. Eiders have similar Δ¹⁹⁹Hg as killifish but much higher δ²⁰²Hg, suggesting that there is an internal fractionation of δ²⁰²Hg in birds. Our study shows that Hg isotopes can be used to identify multiple anthropogenic inorganic Hg and MMHg sources and determine the degree of photodegradation of MMHg in estuarine food webs.