Hydroacoustics is widely used in fisheries research particularly for broad scale investigations such as fish stock assessments. There has, however, only been limited use of such technologies on a smaller scale for estimations of fish abundance, biomass and population size structures inside versus outside marine protected areas (MPAs). Further, within these, understanding the effects of habitat on fish distribution is of high importance especially in movements towards ecosystem based fisheries management (EBFM). The central aim of this study was to use hydroacoustic methods to determine fish distribution in and around existing MPAs and to identify areas which may be suitable for future protection. This was achieved through three field studies described in this thesis. The first study based at multiple locations across The Cayman Islands, examines in a spatial context the protection that MPAs afford to fish spawning aggregations (FSAs) of Nassau grouper (Epinephelus striatus) that they are designed to safeguard. The study found acoustic abundance estimates were similar to those made by divers. The results show the efficacy of hydroacoustic methods for FSA monitoring. The second study was centred on the Cabo Pulmo National Park (CPNP) in Baja California, Mexico. This study details the first application of hydroacoustics for MPA assessment. The results showed that fish abundance and biomass were significantly higher within the CPNP than nearby control areas. Further, the reefs within the CPNP had an order of magnitude greater abundance and biomass, demonstrating the importance of both habitat and protection for fish populations. The third field study was in the waters of the Qatari Gulf, where the hydroacoustic method was used to assess fish abundance values over different habitats to potentially determine areas suitable for protection. The results showed fish abundance, biomass and mean size were greatest over more complex habitats. The final data Chapter examines the data from the three field studies through a size spectra approach. This chapter details the first use of examining hydroacoustically derived fish size spectra in the marine environment. Fish size spectra was more curvilinear over more rugose habitats. This, in combination with examination of the slopes and heights of the spectra has shown that hydroacoustic size spectra approach may be of great value for rapidly assessing the status of fish communities in a non-destructive manner.