It has been demonstrated that intensive fishing, i.e., removing more than 25% of the fish biomass, can reduce mercury levels in predator fish in a lake. We test here the hypothesis that, by removing an important part of the fish biomass from a lake, a significant amount of methylmercury can be eliminated, therefore reducing the mercury available to the remaining biota, at least in the short term. A mass burden approach is used to evaluate the partitioning of total mercury and methylmercury in natural lake ecosystems. Three small natural lakes from the James Bay territory, in northern Québec, Canada, were selected for intensive fishing. Mercury (Hg) and methylmercury (MeHg) concentrations were evaluated for sediments, water column (dissolved fraction and suspended particulate matter), plankton, aquatic invertebrates, and fish. Biomasses were determined for fish, plankton, and aquatic invertebrates. Two case scenarios are presented using different mercury contributions from the sediment component (1 cm depth, and no sediment). Our results for the scenario including the sediment contribution show that lake sediments represent over 98% of the total mercury while the biotic components represent less than 0.1% of the same burden. For methylmercury, fish account for up to 5% of the burden, while sediments make up 84.6% to 93.1%. If we put aside the sediment contribution, the methylmercury in fish partitioning can represent up to 48%. As for invertebrates, they can account for up to 48% of the total MeHg burden. We do not observe any change in the partitionings or the quantities of Hg and MeHg before and after fishing in either of the two case scenarios even when we do not take into account dynamics of the ecosystems. This will be all the more the case when the dynamics of the system are included in the analyses. Therefore, biological parameters such as growth rates or fish diet must be considered.