In the past, the coastal leaky aquifer system, including two aquifers and an aquitard between them, was commonly assumed to be homogeneous and of infinite extent in the horizontal direction. The leaky aquifer system may however be heterogeneous and of finite extent due to variations in depositional and post depositional processes. In this paper, the leaky aquifer system is divided into several horizontal regions for the heterogeneous aquitard and underlying aquifer. A one-dimensional analytical model is developed for describing the head fluctuation in such a heterogeneous leaky aquifer system. The hydraulic head of the upper unconfined aquifer is assumed constant. It is found that both the length and location of the discontinuous aquitards presented in the coastal area have significant effects on the amplitude and phase shift of the head fluctuation in the lower aquifer. In addition, the influence of the formation heterogeneity on the spatial head distribution is also investigated.