There is no established approach for dealing with the active acoustic detection of biological targets in highly dynamic aquatic environments where intense physical interference means that standard techniques are unsuitable. This is a particular problem in ecologically important environments with emerging industrial significance such as marine energy extraction sites. We developed an automatic processing method which allows effective target detection with high sensitivity throughout variable acoustic conditions. The method is based on scale-dependent adaptive filtering of data and morphological analysis of short-scale backscatter contributions for the exclusion of intense turbulent features and isolation of biological targets. Echosounder platform deployments around marine energy infrastructure in a tidal channel provide test data which demonstrate the effectiveness of the proposed approach. Target validation and assessment is carried out by the analysis of multifrequency characteristics and direct inspection. The results deliver effective, quantitative, and repeatable assessment of ecological interactions and target distributions with clear implications for environmental assessment in high energy sites and promising applications in other contexts.