Despite the wide application of riparian buffers in the managed boreal forest, their long-term effectiveness as freshwater protection tools remains unknown. Here, we evaluate windthrow incidence in riparian buffers in the eastern Canadian boreal forest and determine the effect of windthrow on the water quality index of the adjacent freshwater ecosystems. We studied 40 sites—20 riparian buffers, aged 10 to 20 years after harvesting and 20 control sites within intact riparian environments—distributed among clay and sandy (esker) soils and black spruce (Picea mariana) and jack pine (Pinus banksiana) stands. We observed more windthrow in the harvested stands (36%) relative to the control sites (16%), regardless of substrate and species. We determined that the most important factors explaining windthrow were exposition, harvesting, aquatic environment size, and stand characteristics. These factors drive wind exposure, speed, and force, which determine post-harvest windthrow risk. Furthermore, windthrow negatively affected the water quality index of the adjacent aquatic systems, i.e., greater windthrow decreased the protective effect of the riparian buffer. We recommend increasing the use of partial harvest near riparian environments and adapting riparian buffers to site conditions to ensure the long-term protection of adjacent freshwater ecosystems.