Despite rapid development of marine renewable energy, relatively little is known of the immediate and future impacts on the surrounding ecosystems. Quantifying the behavior and distribution of animals around marine renewable energy devices is crucial for understanding, predicting, and potentially mitigating any threats posed by these installations. The Flow and Benthic Ecology 4D (FLOWBEC) autonomous seabed platform integrated an Imagenex multibeam echosounder and a Simrad EK60 multifrequency echosounder to monitor marine life in a 120∘ sector over ranges up to 50 m, seven to eight times per second. Established target detection algorithms fail within MRE sites, due to high levels of backscatter generated by the turbulent physical dynamics, limiting and biasing analysis to only periods of low current speed. This study presents novel algorithms to extract diving seabirds, fish, and fish schools from the intense backscatter caused by turbulent dynamics in flows of 4 m s−1. Filtering, detection, and tracking using a modified nearest neighbor algorithm provide robust tracking of animal behavior using the multibeam echosounder. Independent multifrequency target detection is demonstrated using the EK60 with optimally calculated thresholds, scale-sensitive filters, morphological exclusion, and frequency-response characteristics. This provides sensitive and reliable detection throughout the entire water column and at all flow speeds. Dive profiles, depth preferences, predator–prey interactions, and fish schooling behavior can be analyzed, in conjunction with the hydrodynamic impacts of marine renewable energy devices. Coregistration of targets between the acoustic instruments increases the information available, providing quantitative measures including frequency response from the EK60, and target morphology and behavioral interactions from the multibeam echosounder. The analyses draw on deployments at a tidal energy site in Scotland to compare the presence and absence of renewable energy structures across a range of physical and trophic levels over complete spring-neap tidal cycles. These results can be used to inform how animals forage in these sites and whether individuals face collision risks. This quantitative information can de-risk the licensing process and, with a greater mechanistic understanding at demonstration scales, its predictive power could reduce the monitoring required at future arrays.