A mass balance model for mercury in Lake Champlain was developed in an effort to understand the sources, inventories, concentrations, and effects of mercury (Hg) contamination in the lake ecosystem. To construct the mass balance model, air, water, and sediment were sampled as a part of this project and other research/monitoring projects in the Lake Champlain Basin. This project produced a STELLA-based computer model and quantitative apportionments of the principal input and output pathways of Hg for each of 13 segments in the lake. The model Hg concentrations in the lake were consistent with measured concentrations. Specifically, the modeling identified surface water inflows as the largest direct contributor of Hg into the lake. Direct wet deposition to the lake was the second largest source of Hg followed by direct dry deposition. Volatilization and sedimentation losses were identified as the two major removal mechanisms. This study significantly improves previous estimates of the relative importance of Hg input pathways and of wet and dry deposition fluxes of Hg into Lake Champlain. It also provides new estimates of volatilization fluxes across different lake segments and sedimentation loss in the lake.