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The Tuolumne River Watershed recently experienced several large, anthropogenic forest fires including the Rim Fire. These hot, intense fires contributed to increased fine sediment in the Clavey and Mainstem Tuolumne rivers. The deposition and accumulation of fine sediment in various hydrologic zones affected aquatic biota such as benthic algae and macroinvertebrates by reducing substrate habitability through increased siltation. An adaptive management strategy that includes controlled burns, increased fire safety near development, and removal of heavy fuel loads would help reduce occurrences of these unnaturally-amplified large fire events and protect the integrity of the river’s flow regime, habitats, and ecological communities.