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Where marine waters are shallow and bathymetric features are steep, the typically employed multi-beam side scan sonar is not always reliable for identifying complex biological structures. Here, we present a cost-efficient method used in Howe Sound, British Columbia, for bathymetric mapping, exploration, and ground-truthing of glass sponge bioherms. A simple depth sounder and software package was used to produce bathymetric maps. From these maps, prospective sites were selected and surveyed to investigate bioherm presence with a simple drop-camera towed off the bow of a small drifting vessel during calm seas. This method was used during a 4-year citizen science initiative that led to the discovery of 12 glass sponge bioherms in Howe Sound, the first step in protecting these globally unique reefs from the impact of bottom-contact fishing, anchoring, and potential industrial contamination. Before our work using this method, only two glass sponge bioherms had been identified in Howe Sound. The method also proved effective as a means to quantify damage to bioherms from fishing gear.