This paper discusses the utility of using seismic-reflection profiling and sediment cores in addition to bottom grab samples and acoustic data to develop shallow-water benthic habitat maps. Currently, the classification system used herein does not provide for the incorporation of stratigraphic data, but we believe that the utility of these maps would improve if such data were included. We conducted vessel-based seafloor-mapping surveys using a phase-measuring sidescan sonar in very shallow waters (mean depth = 3.2 m) covering an area >6.7 km² in Pleasant Bay in 2014. We collected a total of 192 bottom grab samples to document macro-invertebrates and sediment characteristics. We conducted seismic-reflection profiling surveys to document stratigraphy and determine optimal locations for multiple sediment cores during the 2014 field season; we collected both Kullenberg and Livingstone cores. The seismic-reflection data, though conducted at the reconnaissance scale, proved useful to place the seafloor acoustic data in context. The acoustic and benthic habitat data and mapping products become more valuable when an understanding of the underlying stratigraphy is used as context for the benthic habitat maps. Sediment coring and analysis can provide insights into past and current basin evolution, which can further aid marine natural resource managers. However, we believe that stratigraphic data should be incorporated into standard benthic habitat mapping protocols. These multi-modal datasets provide a better understanding of these habitats for the multidisciplinary teams that typically produce and use these maps as well as coastal managers.