The flow resistance of steep open channels featuring step-pool morphology was investigated with special consideration of the effect of bed-load transport. For the investigated parameter reach, steep slopes of 5 to 11% and a broad grain size distribution, bed-load transport reduces flow resistance. Bed-load fills pools and smoothens the bed surface. This inhibits energy dissipation in pools and at large protruding boulders. Non-dimensional hydraulic geometry equations for both clear-water and flow with bed-load are proposed. A comparison of the new equations indicates a change in the main energy dissipation mechanism for flows with bed-load. It was observed that the increased flow velocity for bed-load flow leads to the mobilization of step forming boulders. The total destruction of step-pool sequences always occurred at critical or near critical flow conditions. The implications of the flow resistance reducing effect of bed-load on the bed stability is discussed and compared with existing stability approaches.