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ABSTRACT Critical data concerning key developments in global human history now lie submerged on continental shelves where investigations confront significant challenges. Whereas underwater excavations and surveys are expensive and weather dependent and require specialized training and equipment, remote sensing methods can improve chances for success offshore. A refinement in one method, a semi‐automated analysis protocol that can help to identify Pleistocene and Holocene era archaeological deposits in bathymetric LiDAR datasets, is presented here. This method employs contour mapping to identify potential archaeological features in shallow water environments in Apalachee Bay, Florida. This method successfully re‐identified multiple previously recorded archaeological sites in the study region and detected at least four previously undocumented archaeological sites. These results suggest that this procedure can expand on methods to identify and record submerged archaeological deposits in sediment‐starved, shallow‐water environments.