Underwater communication relies on acoustic links due to its long propagation and low attenuation properties. Despite the advantages of using acoustic links over radio frequency (RF), the major drawback is the limited bandwidth of the acoustic spectrum. To circumvent this, we advocate the use of directional antennas rather than the traditional omni-directional antennas to boost the network throughput by taking advantage of the spatial spectrum. In this paper, we analyze the network throughput for shallow water communication with directional antennas. Unlike traditional line-of-sight (LOS) directional communication, our analysis will aim to factor in non-line-of-sight (NLOS) links in the throughput analysis. We will be focusing on two NLOS links; namely refracted-surface-reflected (RSR) and refracted-bottom-reflected (RBR) to study the multipath effects on the network throughput. Simulation experiments are also provided to validate the analytical results.