Understanding the abundance and distribution of fish in tidal energy streams is important for assessing the risk presented by the introduction of tidal energy devices into the habitat. However, the impressive tidal currents that make sites favorable for tidal energy development are often highly turbulent and entrain air into the water, complicating the interpretation of echosounder data. The portion of the water column contaminated by returns from entrained air must be excluded from data used for biological analyses. Application of a single algorithm to identify the depth-of-penetration of entrained-air is insufficient for a boundary that is discontinuous, depth-dynamic, porous, and widely variable across the tidal flow speeds which can range from 0 to 5m/s. Using a case study at a tidal energy demonstration site in the Bay of Fundy, we describe the development and application of deep learning models that produce a pronounced, consistent, substantial, and measurable improvement of the automated detection of the extent to which entrained-air has penetrated the water column. Our model, Echofilter, was highly responsive to the dynamic range of turbulence conditions and sensitive to the fine-scale nuances in the boundary position, producing an entrained-air boundary line with an average error of 0.32m on mobile downfacing and 0.5-1.0m on stationary upfacing data. The model's annotations had a high level of agreement with the human segmentation (mobile downfacing Jaccard index: 98.8%; stationary upfacing: 93-95%). This resulted in a 50% reduction in the time required for manual edits compared to the time required to manually edit the line placed by currently available algorithms. Because of the improved initial automated placement, the implementation of the models generated a marked increase in the standardization and repeatability of line placement.