Environmental interactions of marine renewable energy developments vary from fine-scale direct (e.g. potential collision) to indirect wide-scale hydrodynamic changes altering oceanographic features. Current UK Environmental Impact Assessment (EIA) and associated Habitats Regulations Appraisal (HRA) guidelines have limited focus on underlying processes affecting distribution and movements (hence vulnerability) of top predators. This study integrates multi-trophic ship survey (active acoustics and observer data) with an upward-facing seabed platform and 3-dimensional hydrodynamic model as a process-driven framework to investigate predator-prey linkages between seabirds and fish schools. Observer-only data highlighted the need to measure physical drivers of variance in species abundances and distributions. Active acoustics indicated that in situ (preferable to modelled) data were needed to identify temporal changes in hydrodynamics to predict prey and consequently top predator presence. Revising methods to identify key habitats and environmental covariates within current regulatory frameworks will enable more robust and transferable EIA and HRA processes and outputs, and at larger scales for cumulative and strategic-level assessments, enabling future modelling of ecosystem impacts from both climate change and renewable energy extraction.