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This thesis develops analytical frameworks for evaluating the validity of MBES data with comparable ground truthing and hydrodynamic data with respect to geomorphology and marine biodiversity in two Special Areas of Conservation (SAC) in the Malin-Hebrides Sea off the north-Irish coast. First, a modelling framework based on Generalised Linear Modelling (GLM) is developed to test the validity of multi-frequency MBES backscatter data (30, 95, 300 kHz) to characterise sediment grain size in the Hempton's Turbot Bank (HTB) SAC. The results demonstrate that the single-frequency sources have a marginal gain on the multi-frequency model, with the 30 kHz model driving the significance of the multi-frequency model, and the inclusion of the higher frequencies diminishes the level of agreement. Secondly, a combination of K-Means unsupervised classification and GLM based on MBES backscatter (95, 300 kHz) and bathymetry analysis are successfully used to predict different levels of sandeel Hyperoplus lanceolatus densities with respect to geomorphology in the HTB SAC. The study demonstrates that the lower frequency source is more adept at capturing the variety inherent in shallow sub-surface sedimentary environments, which this species prefers. Finally, multidisciplinary modelling and analysis approaches using MBES data, hydrodynamic data and theodolite tracking observations are used to assess the spatial dynamics of harbour porpoise Phocoena phocoena in the Skerries and Causeway SAC. Generalised Additive Modelling (GAM) identifies that slope, aspect and backscatter intensity are the most statistically significant variables accounting for the highest deviance in porpoise sighting density. Models predict a high probability (> 0.6) of porpoise encounters in nearshore areas, particularly concentrated around headlands where local flow acceleration results in coarser beds. The robust workflows developed in this thesis, provides a proof of concept for developing robust monitoring strategies for Marine Protected Areas and associated species. Respective recommendations will inform marine policy, marine spatial planning and management.