Concerns over the fate and bioaccumulation of mercury (Hg) inputs to Onondaga Lake, a hypereutrophic lake in central New York, prompted an investigation into the concentrations and fluxes of Hg discharge from the Onondaga County Metropolitan Wastewater Treatment Plant (METRO WWTP). Discharge of methyl Hg (MeHg) is of concern because it is the form of Hg that readily bioaccumulates along the aquatic food chain. This study incorporated clean protocols for sampling and Hg analysis to evaluate: seasonal patterns in the concentrations of total Hg (THg) and MeHg in the WWTP unit processes; the production of MeHg within the unit processes of the WWTP; the overall fate of THg and MeHg within the WWTP; and the relative impact of the Hg discharged from the WWTP to Onondaga Lake. Concentrations of THg (range: 80–860 ng/L) and MeHg (0.7–17 ng/L) in raw sewage were highly variable, with higher concentrations observed in the summer months. The dynamics of THg though the WWTP were correlated with total suspended solids (TSS). As a result, the majority of the THg removal (55%) occurred during primary treatment. Overall, about 92% of the THg entering the plant was removed as sludge, with volatilization likely a minor component of the overall Hg budget. The transformation of MeHg through the plant differed from THg in that MeHg was not correlated with TSS, and displayed strong seasonal differences between winter (November to April) and summer (May–October) months. During the summer months, substantial net methylation occurred in the activated sludge secondary treatment, resulting in higher MeHg concentrations in secondary effluent. Net demethylation was the dominant mechanism during tertiary treatment, resulting in removal of substantial MeHg from the secondary effluent. The overall MeHg removal efficiency through the plant was about 70% with more efficient removal during summer months. Sediment trap collections made below the epilimnion of Onondaga Lake indicated average deposition rates of 12 μg/m 2-day for THg and 0.33 μg/m 2-day for MeHg. These deposition rates are more than an order of magnitude higher than the thermocline area normalized external loads from METRO effluent (0.85 μg/m 2-day for THg, 0.05 μg/m 2-day for MeHg). Our findings indicate that the impact of the discharge from METRO is relatively small, contributing about 10–15% of Hg to the total gross Hg input to the hypolimnion of the lake.