In this paper, pore pressure distributions of two-layer porous soil under nonlinear harmonic waves are presented. The governing equations are written in their fully dynamic form and the possible simplifications are introduced. Finite element models are developed for each formulation and numerical results are verified with their corresponding analytical solutions for the two-layer case. Then the problem of a two-layer soil system under waves both in free field and in front of a vertical wall is studied in terms of dynamic pore pressure response. Here both linear and non-linear waves are considered. Finally, a number of parametric studies to investigate the effect of wave non-linearity on the dynamic behavior are carried out. The results indicate that two-layer response is significantly different from that of a conventional single layer approach and wave non-linearity has significant effects in both free field response and in the presence of a wall.