Riparian zones contain areas of strong hydrological connectivity between land and stream, referred to as variable source areas (VSAs), and are considered biogeochemical control points. However, little is known about whether VSAs influence stream communities and whether this connectivity is affected by forest management. To address this, we used multiple biotic and abiotic indicators to (1) examine the influence of VSAs on riparian vegetation and stream ecosystems by comparing VSA and non-VSA reaches and (2) explore how forest management may affect the influence of VSAs on stream ecosystems. We detected some significant differences between VSA and non-VSA reaches in the riparian vegetation (greater understory and lower tree density) and stream ecosystem indicators (greater dissolved organic matter aromaticity, microbial biomass, peroxidase activity and collector-gatherer density, and lower dissolved organic carbon concentrations, algal biomass, and predatory macroinvertebrate density), which suggests that VSAs may create a more heterotrophic ecosystem locally. However, we show some evidence that forest management activities (specifically, road density) can alter the influence of VSAs and eliminate the differences observed at lower forest management intensities, and that the most hydrologically connected areas seem more sensitive to disturbance. Therefore, we suggest that the heterogeneity in hydrological connectivity along riparian zones should be considered when planning forest harvesting operations and road building (e.g., wider riparian buffers around VSAs).