Effects of water velocity on the accumulation of periphyton and silt were investigated in two unenriched rivers (Tongariro and West Kowai Rivers) of New Zealand. Artificial substrata were incubated for up to 5 weeks in areas of moderate (0.2–0.5 m s−1) and high (0.6–0.9 m s−1) velocity. In the Tongariro River, periphyton accrual was significantly higher in moderate velocities than in high velocities, but not in the West Kowai River. The accumulation of silt was significantly higher under the moderate velocity treatment in both rivers. Silt densities were closely correlated with periphyton chlorophyllaand stepwise multiple regression analysis indicated that periphyton biomass was a more significant determinant of silt densities than water velocity. Neither chlorophyllanor silt densities showed any significant variation with depth within the ranges measured (0.2–0.6 m). Several floods occurred during the study period and these, together with water velocities greater than c. 0.3 m s−1, tended to affect periphyton ash‐free dry mass (AFDM) and silt more than they affected chlorophylla.It appeared that growing periphyton were resisting the effects of high shear stress and that unattached inorganic and organic particles were flushed from the periphyton matrix during higher flows. Spatial variation in periphyton and silt accrual as functions of velocity and depth were too variable to be useful for prediction of abundance and distribution using hydraulic‐habitat models.