Barbel and gudgeon differ in their biology and ecology so that their bioturbation of streambed sediments may have specific effects on the patch dynamics of the sediment transport. Using experimental streams, we tested this idea by measuring the impact of a naturally occurring biomass gradient of each fish on the (1) transport of gravel and sand at base flow; (2) sediment surface characteristics; and (3) critical shear stress (τC) causing incipient gravel and sand motion during simulated floods. Corresponding to their biology and ecology, the fish specifically modified base flow transport and surface of the sediments. The greatest τC reduction for gravel/sand caused through these base flow fish activities was ~50%/~60% in the barbel and ~35%/~60% in the gudgeon experiment. We integrate these results into a conceptual framework that outlines the contribution of benthic animals to the patch dynamics of the gravel and sand transport in real streams.