For many hydraulic engineering problems, the analysis of resistance to free-surface flow over gravel-paved riverbeds, especially over boulders protruded riverbeds, is a fundamental prerequisite. Computational equations on the resistance to flow were developed from the Darcy-Weisbach equation by using experimental results on flows with large-scale roughness elements installed in a wide laboratory channel. A design method of boulders protruded slope fishways is presented that is based on investigation results of the flow resistance of large-scale roughness elements. A numerical example for designing fishways is presented to illustrate a calculation procedure.