To better understand the complex process of wave transformation and associated hydrodynamics over various fringing reef profiles, numerical experiments were conducted with a one-dimensional(1D) Boussinesq wave model. The model is based on higher-order Boussinesq equations and a higher-accuracy finite difference method. The dominant energy dissipation in the surf zone, wave breaking, and bottom friction were considered by use of the eddy viscosity concept and quadratic bottom friction law, respectively. Numerical simulation was conducted for a wide range of wave conditions and reef profiles. Good overall agreement between the computed results and the measurements shows that this model is capable of describing wave processes in the fringing reef environment. Numerical experiments were also conducted to track the source of underestimation of setup for highly nonlinear waves. Linear properties(including dispersion and shoaling) are found to contribute little to the underestimation; the low accuracy in nonlinearity and the ad hoc method for treating wave breaking may be the reason for the problem. To better understand the complex process of wave transformation and associated hydrodynamics over various fringing reef profiles, numerical experiments were conducted with one-dimensional (1D) Boussinesq wave model. The model is based on higher-order Boussinesq equations and a higher-accuracy finite difference method. The dominant energy dissipation in the surf zone, wave breaking, and bottom friction were considered by use of the eddy viscosity concept and quadratic bottom friction law, respectively. Numerical simulation was conducted for a wide range of wave conditions and reef profiles. Good overall agreement between the computed results and the measurements shows that this model is capable of describing wave processes in the fringing reef environment. shoaling) are found to to little to the underestimation; the low accuracy in nonlinearity and the ad hoc method for treating wave breaking may be the reason for the problem.