The goal of this study was to examine how the implementation of boulders can regulate the influx, transport and deposition of fine sediment in gravel-bed rivers. Generic experiments were performed in a laboratory flume, with and without the presence of partially-submerged boulders. Experimental results showed: (1) boulders regulated the depositional patterns of the incoming sediment by the formation of characteristic sand patches in their stoss region; (2) significant reduction in the bedload rates was observed due to the presence of boulders and sand depositional features; and (3) less sand accumulated within the bed when boulders were present. The above findings illustrate that boulders can create a sustainable aquatic environment by acting as barriers of the incoming sediment and by offering protection to the highly productive spawning gravels used by fish to spawn their eggs.