We study the software simulation of physical properties of underwater communications, namely, underwater acoustic waves and (de)modulation of underwater acoustic digital data signals. We take into account the mobility of nodes, present in underwater sensor networks. We also consider the integration with protocol layers above the physical layer, i.e., the link and network layers. In this context, mobility is relevant because there are underwater vehicles and environmental conditions causing displacements of sensors. Attenuation is sensitive to transmitter-receiver separation distance. Because of mobility, this separation distances is variable. Our simulation approach is based on the work of Borrowski (2010). The physical layer is modeled as MATLAB functions. As a function of distance and frequency, the model takes into account attenuation, noise and their effects on a phase-shift keying signal. We use OMNeT++ to model link and network layer protocols. The MATLAB functions and OMNet++ models are linked together. While MATLAB does particularly well with signal processing, OMNeT++ addresses better the protocols placed in the link layer and above