In Ontario’s boreal forest, guidelines for forest management practices focus primarily on the conservation of biodiversity, with many guidelines having the added benefit of reducing potentially harmful changes to local hydrology and biogeochemistry. Many of these added benefits remain untested experimentally. Here, we discuss the results of a 3-year study in northwestern Ontario wherein several small watersheds were monitored prior to, during and after harvest for streamflow, as well as concentrations of total mercury, methylmercury and several other metals. Nearby unharvested reference watersheds were similarly monitored and compared with harvested watersheds over the same period to control for inter-annual climatic variability. Watersheds were harvested following provincial guidelines, but there were major differences across watersheds in relation to properties such as the proportion of watershed area harvested, road construction density and buffer strip width. Watersheds with lesser harvest, fewer roads and greater buffer protection resulted in small to no changes in mercury and metal concentrations and loadings when comparing pre- to post-harvesting periods. The greatest effects on concentrations and loadings were observed where small and unmapped streams were protected only by a 3 m “machine exclusion zone” and where multiple inadvertent or necessary stream crossings led to major soil disturbance by machinery. Overall, the management of upland erosion and the potential connectivity of newly wetter near-stream areas are important considerations for better protecting stream biota from increased metal concentrations and inputs.