Prediction methods of flow resistance and bed-load transport rate in alluvial streams with sand waves under lower-regime are proposed in this study. At first, the skin friction equation is derived by integrating the bed shear stress distribution equation on a sand wave surface. We propose the equation of hydraulic resistance based on the equations of skin friction and form drag next. The hydraulic resistance equation is verified with estimations of mean depth of flow over sand waves. The reach averaged bed-load transport rate can be calculated reasonably by the Meyer Peter & Müller’s equation using the proposed skin friction equation with the estimated mean flow depth. The proposed method in this study can predict flow depth, geometrical scale of sand waves, and bed-load transport rate by giving water discharge, bed gradient and grain diameter. The proposed method also clarifies that the ratio of a form drag to a skin friction for sand waves is different in a uniform sediment bed and a non-uniform sediment bed.