Concerns about mercury (Hg) contamination in Lake Whatcom, Washington, were raised in the late 1990s after a watershed protection survey reported elevated concentrations of Hg in smallmouth bass. The U.S. Geological Survey, the Whatcom County Health Department, and the Washington State Department of Ecology (Ecology) cooperated to develop a study to review existing data and collect new data that would lead to a better understanding of Hg deposition to Lake Whatcom and other lakes in Whatcom County, Washington. A simple atmospheric deposition model was developed that allowed comparisons of the deposition of Hg to the surfaces of each lake. Estimates of Hg deposition derived from the model indicated that the most significant deposition of Hg would have occurred to the lakes north of the City of Bellingham. These lakes were in the primary wind pattern of two municipal waste incinerators. Of all the lakes examined, basin 1 of Lake Whatcom would have been most affected by the Hg emissions from the chlor-alkali plant and the municipal sewage-sludge incinerator in the City of Bellingham. The length-adjusted concentrations of Hg in largemouth and smallmouth bass were not related to estimated deposition rates of Hg to the lakes from local atmospheric sources. Total Hg concentrations in the surface sediments of Lake Whatcom are affected by the sedimentation of fine-grained particles, whereas organic carbon regulates the concentration of methyl-Hg in the surface sediments of the lake. Hg concentrations in dated sediment core samples indicate that increases in Hg sedimentation were largest during the first half of the 20th century. Increases in Hg sedimentation were smaller after the chlor-alkali plant and the incinerators began operating between 1964 and 1984. Analysis of sediments recently deposited in basin 1 of Lake Whatcom, Lake Terrell, and Lake Samish indicates a decrease in Hg sedimentation. Concentrations of Hg in Seattle precipitation and in tributary waters were used to calculate current (2002-03) loadings of Hg to Lake Whatcom. Hg in tributaries contributed 59 percent of the total Hg, whereas non-local atmospheric deposition was estimated to have contributed 41 percent of the 303 grams of Hg entering Lake Whatcom each year. However, these inputs cannot be verified without a better understanding of the sources of sediment to Lake Whatcom.