To design a coastal structure in the nearshore region, engineers must have means to estimate wave climate. Waves, approaching the surf zone from offshore, experience changes caused by combined effects of bathymetric variations, interference of man-made structure, and nonlinear interactions among wave trains. This paper has attempted to find out the effects of two of the more subtle phenomena involving nonlinear shallow water waves, amplitude dispersion and secondary wave generation. Boussinesq-type equations can be used to model the nonlinear transformation of surface waves in shallow water due to effects of shoaling, refraction, diffraction, and reflection. In this paper, generalized Boussinesq equations under the complex bottom condition is derived using the depth averaged velocity with the series expansion of the velocity potential as a product of powers of the depth of flow. A time stepping finite difference method is used to solve the derived equation. Numerical results are compared to hydraulic model results. The result with the non-linear dispersive wave equation can describe an interesting transformation a sinusoidal wave to one with a cnoidal aspect of a rapid degradation into modulated high frequency waves and transient secondary waves in an intermediate region. The amplitude dispersion of the primary wave crest results in a convex wave front after passing through the shoal and the secondary waves generated by the shoal diffracted in a radial manner into surrounding waters.