Recently, the drainage of urbanized area is planned by underground conduit networks. Then, we have to know more about the flow structure in a circular pipe with free-surface and/or deposit layer. In this study, the velocity measurements were conducted for flow with a free surface and a deposit layer in a circular pipe, where not only the cross-sectionally averaged velocity but also the cross-sectional distribution of velocity. On the other hand, a numerical analysis of flow was conducted, where the algebraic stress turbulence model was employed because of its composite boundaries with different roughness. The conditions for respective boundaries became an important problem. Particularly, the boundary condition at the free surface was investigated to get a convenient way for numerical analysis of flow with free surface and deposit layer, where the location with maximum velocity appears beneath the free surface and it would be estimated by calculation.