The advance of tidal energy technologies has created new demands for active acoustic monitoring in highly dynamic marine environments. An innovative data collection approach using the FLOWBEC multi-instrument platform has been developed to acoustically observe turbulence and ecological interactions in the challenging environments around turbine installations in the UK. Standard processing approaches for echosounder data are unsuitable in these sites because of the extreme variability in acoustic conditions due to strong tidal flows and complex wind-wave interactions. Novel techniques for identifying ecological targets (fish, diving seabirds, and marine mammals) and characterising the physical conditions have been developed which are functional even during extreme turbulence. Reliable target identification is achieved using scale-sensitive filtering, morphological characterization, and multifrequency analysis of EK60 echosounder data. Combining results with synchronized multibeam data and other observations gives new oceanographic and ecological insights into these environments. This study contributes novel methodological and processing concepts for acoustic analysis in challenging sites of emerging industrial importance. The results provide vital observations on the behaviour of marine species with clear applications for the analysis of environmental impacts of marine renewable energy technologies.