A model harbour with Plan scale of $1.08{ imes}1.08m$ is built on a tidal tank using a Froude relationship from a real harbour($432{ imes}432m$). Velocity components are measured by a ultrasonic velocity meter and flow structure is then predicted using a 2-D depth integrated hydrodynamic model. In the finite difference model implemented in this study, various wall boundary conditions, i.e. no-slip, free-slip, partial-slip and semi-slip are used to represent turbulent diffusion terms, e.g. ${partial}^2U_{ij}/{partial}x^2;or;{partial}^2U_{ij}/{partial}y^2$. These conditions are focused to investigate their influence on the flow structure along the wall and basin of the harbour with aspect ratio of unity, i.e. Length/Breadth. Numerical experiments are compared with the measurements and used to analyse flow patterns in the basin during tidal cycles. It is shown from the results that no-slip closed boundary condition is the most appropriate method with respect to the location of the eddy centre, although the condition underestimates velocity components along the wall.