Nonlinear free surface flow phenomena have been studied by several kinds of numerical methods, of which boundary element method has been known as most promising one. There, however, remain many difficulties to be solved in the numerical procedures by boundary element analysis. In this paper, an efficient calculation of elemental integrals and iterative solution algorithm for the resulting system of equations were thoroughly investigated in order to enhance the procedure of the boundary element analysis. Advantages of the herein developed boundary element analysis code are demonstrated in terms of accuracy and convergence for typical boundary-value problems with free surface.