Our objective was to examine how the behavior of atmospheric mercury (Hg) deposited to boreal lake mesocosms changed over time. We added inorganic Hg enriched in a different stable isotope in each of two years, which allowed us to differentiate between Hg added in the first and second year. Although inorganic Hg and methylmercury (MeHg) continued to accumulate in sediments throughout the experiment, the availability of MeHg to the food web declined within one year. This decrease was detected in periphyton, zooplankton, and water mites, but not in gomphid larvae, amphipods, or fish. We suggest that reductions in atmospheric Hg deposition should lead to decreases in MeHg concentrations in biota, but that changes will be more easily detected in short-lived pelagic species than long-lived species associated with benthic food webs.