An important consequence of reservoir creation is the production and bioaccumulation of neurotoxic methylmercury through the food web into fish. The FLooded Upland Dynamics EXperiment (FLUDEX) at the Experimental Lakes Area in NW Ontario tested the hypothesis that methylmercury production in reservoirs is related to the amount and decomposition of flooded organic matter. From 1999-2001, three upland forests that varied in the amounts of organic carbon stored in vegetation and soils were flooded from spring to autumn with low organic carbon, low methylmercury water pumped from a near-by lake. Within the framework of the FLUDEX, this study examined whole-reservoir rates of methylation or demethylation based on net methylmercury exports from reservoirs and methylmercury pools in soils, periphyton, zooplankton and fish. This whole-ecosystem scale research was complemented with two smaller studies designed to examine the process of mercury methylation in reservoirs. This study can assist hydroelectric utilities in making informed decisions about site selection for future reservoir development to reduce mercury contamination of reservoir fisheries.