Environmental disturbances like deforestation or climate change may influence lake thermal and oxic stratification, thereby modifying cycles of contaminants such as mercury (Hg). In a lake naturally separated into three basins, the thermocline and oxycline of an experimental basin were deepened by 4 and 3 m, respectively, to study the effect on the methylmercury (MeHg) accumulation. This treatment decreased hypolimnetic MeHg concentration by approximately 90%, zooplankton concentrations by 30 to 50%, and in some fish by 45%. A multiple linear regression indicated that oxycline depth significantly influenced hypolimnetic MeHg concentrations, with no significant effect of thermocline depth, anoxic water volume, interface area of oxic-anoxic water, and sediment area in contact with anoxic water. Fish MeHg decline varied, with a greater response by low oxygen-tolerant bullhead. Increased pelagic primary and secondary production likely caused zooplankton and fish MeHg decreases via algal and growth dilution. Environmental changes leading to oxycline deepening are therefore predicted to cause a decrease in MeHg bioaccumulation in similar Canadian Shield lakes. If associated ecosystem impacts related to the deepening treatment are deemed acceptable, then this experiment provides a potential remediation method for small lakes confronted with MeHg accumulation.