Beaver reservoirs and forestry are landscape disturbances that can increase the transfer of mercury (Hg) to stream food webs through increased mobilization from forest soils and methylation within the landscape, and through changes to food web structure. Both disturbances are widespread and co-occur throughout Canada’s boreal region, yet their combined effects on Hg bioaccumulation have not been studied. We sampled upstream and downstream of beaver reservoirs in harvested (n = 3) and non-harvested (n = 3) watersheds in Northwestern Ontario, Canada, for water, food sources (biofilm, leaves, and detritus), macroinvertebrate consumers (herbivorous and predatory), and top predators (fishes). When only harvesting effects were considered (upstream of reservoirs), Hg concentrations ([Hg]) of water, aquatic food sources and consumers, and trophic magnification slopes were highest in harvested compared to non-harvested watersheds; such effects were mostly absent downstream, indicating that effects of beaver reservoirs and harvest were not cumulative. In non-harvested landscapes, significantly higher biotic [Hg] was observed downstream of one reservoir only, potentially due to shifts in consumer diets from terrestrial to aquatic food sources and higher downstream availability of Hg. The most extensively harvested site displayed significant downstream decreases in biotic [Hg] and dissolved organic carbon, while the other two harvested sites had either increases in biotic [Hg], or no changes, indicating that reservoirs vary in their contribution to downstream Hg transfer, but may buffer the overall effects of extensive harvest on downstream Hg dynamics. Results provide new knowledge that helps forest managers incorporate natural disturbances (beaver impoundments) into evaluations and mitigations of forest management impacts on Hg in aquatic food webs.