Experimental flooding of a boreal forest wetland caused the wetland to change from being a small, natural carbon sink, with respect to the atmosphere, of -6.6 g of C m⁻² yr⁻¹ to a large source of +130 g of C m⁻² yr⁻¹. This change was caused by the death of the vegetation, which eliminated the photosynthetic CO₂ sink and stimulated the microbial production of CO₂ and CH₄ from decomposition of plant tissues and peat. Another type of microbial activity that increased was the methylation of inorganic mercury to the much more toxic methyl mercury (MeHg) form. The wetland was a source of MeHg prior to flooding and became an even larger source (39 fold) after flooding. MeHg concentrations in the water sometimes exceeded 2 ng L⁻¹, with the average being 0.9 ng L⁻¹ in the first 2 years after flooding. MeHg also increased in the flooded vegetation and peat, in lower food chain organisms, and in fish. Two recommendations, which should minimize both greenhouse gas production and MeHg production in reservoirs, can be made: (1) minimize the total area of land flooded (i.e., avoid flooding areas of low relief) and (2) minimize the flooding of wetlands, which contain larger quantities of organic carbon than uplands and are sites of intense production of MeHg.