The turbulent structure of flow with small relative submergence, which should be clarified for advanced study of sediment transport in mountain rivers, is different from that with sufficient relative submergence which is familiar to us according to the recent development of research of turbulent open channel flow. In this study, in order to clarify and understand the fundamental mechanism of flow with small relative submergence, turbulence measurements are conducted for flow over a bed composed of glass beads under small relative submergence. The “roughness sublayer” is recognized near the bed where the velocity profile becomes more uniform than the log-law profile and the turbulence is suppressed. These characteristics are attempted to be phenomenologically explained as an influence of eddy sheddings from individual roughness elements on the ordinary wallturbulence.