This paper presents that major computed flow filed above a boundary layer in a surf zone could be strongly affected by kinds of the boundary conditions (slip, non-slip and shift B.C. based on a log law) imposed at a bottom. The estimated bottom shear stress is also considerably dependent on the boundary conditions, which might cause over-or under-predictions for bed-loads transports in the sur-zone. In order to fill a gap between length-scales of predominant turbulent flows over and within the thin boundary layer, a two layer model (TLM) is applied to the boundary layer flows. TLM is found to give the reasonable boundary layer flows and also major flows over the boundary layer. This model may greatly contribute to practical largescale computations typically involving a significant gap of turbulence properties across the boundary layers.