Whilst the development of the tidal stream industry will help meet marine renewable energy (MRE) targets, the potential impacts on mobile marine predators using these highly dynamic environments need consideration. Environmental impact assessments (EIAs) required for potential MRE sites generally involve site-specific animal density estimates obtained from lengthy and costly surveys. Recent studies indicate that whilst large-scale tidal forcing is predictable, local hydrodynamics are variable and often result in spatio-temporal patchiness of marine predators. Therefore, understanding how fine-scale hydrodynamics influence animal distribution patterns could inform the placing of devices to reduce collision and displacement risks. Quantifying distributions requires animal at-sea locations and the concurrent collection of high-resolution hydrodynamic measurements. As the latter are routinely collected during tidal resource characterization at potential MRE sites, there is an untapped opportunity to efficiently collect information on the former to improve EIAs. Here we describe a survey approach that uses vessel-mounted ADCP (Acoustic Doppler current profiler) transects in combination with marine mammal surveys to collect high-resolution and concurrent hydrodynamic data in relation to pinniped (harbour seals Phoca vitulina, grey seals Halichoerus grypus) at-sea occupancy patterns within an energetic tidal channel (peak current magnitudes >4.5 ms−1). We identified novel ADCP-derived fine-scale hydrodynamic metrics that could have ecological relevance for seals using these habitats. We show that our local acoustic backscattering strength metric (an indicator for macro-turbulence) had the highest influence on seal encounters. During peak flows, pinnipeds avoided the mid-channel characterized by extreme backscatter. At-sea occupancy further corresponded with the increased shear and eddies that are strong relative to the mean flows found at the edges of the channel. Our approach, providing oceanographic context to animal habitat use through combined survey methodologies, enhances environmental management of potential MRE sites. The cost-effective collection of such data and the application of our metrics could streamline the EIA process in the early stages of the consenting process.