In-situ capping has shown promise as a management strategy for contaminated aquatic sediments, however, little is known about how mercury methylation in underlying sediments will be affected. Changes to the location and extent of sulfate reduction and other biological processes were studied in estuarine sediment using laboratory microcosms. Observations in a model sediment showed increases of in situ total methylmercury concomitant with an upward extension of anaerobic bacterial activity beneath a sediment cap and under anoxic conditions. Increased methylmercury (up to 50%) was observed beneath a sediment cap in a region 2-3 cm higher than in an uncapped sediment. A 1-dimensional, unsteady, reaction transport model was used to simulate the transient response to mercury-related biogeochemical processes. The location, magnitude, and expected duration of the increased methylmercury was such that a significant impact on near cap-water interface methylmercury was not expected for the sediments studied. Explicit consideration of the biogeochemical effects of capping on mercury contaminated sediment, however, may be necessary for very thin or unstable capping layers where the physical sequestration provided by a cap may be compromised.