Timber harvest has many effects on aquatic ecosystems, including changes in hydrological, biogeochemical, and ecological processes that can influence mercury (Hg) cycling. Although timber harvest’s influence on aqueous Hg transformation and transport are well studied, the effects on Hg bioaccumulation are not. We evaluated Hg bioaccumulation, biomagnification, and food web structure in 10 paired catchments that were either clear-cut in their entirety, clear-cut except for an 8-m wide riparian buffer, or left unharvested. Average mercury concentrations in aquatic biota from clear-cut catchments were 50% higher than in reference catchments and 165% higher than in catchments with a riparian buffer. Mercury concentrations in aquatic invertebrates and salamanders were not correlated with aqueous THg or MeHg concentrations, but rather treatment effects appeared to correspond with differences in the utilization of terrestrial and aquatic basal resources in the stream food webs. Carbon and nitrogen isotope data suggest that a diminished shredder niche in the clear-cut catchments contributed to lower basal resource diversity compared with the reference of buffered treatments, and that elevated Hg concentrations in the clear-cut catchments reflect an increased reliance on aquatic resources in clear-cut catchments. In contrast, catchments with riparian buffers had higher basal resource diversity than the reference catchments, indicative of more balanced utilization of terrestrial and aquatic resources. Further, following timber harvest THg concentrations in riparian songbirds were elevated, suggesting an influence of timber harvest on Hg export to riparian food webs. These data, coupled with comparisons of individual feeding guilds, indicate that changes in organic matter sources and associated effects on stream food web structure are important mechanisms by which timber harvest modifies Hg bioaccumulation in headwater streams and riparian consumers.