Scott Hippensteel's scientific research interests are primarily focused on using microfossils to solve environmental and geoarchaeological problems. Many of his research publications are related to paleotempestology, the study of ancient hurricanes, and factors that influence the records of sea-level rise over the last 10,000 years. More recently he has been applying micropaleontology to archaeological studies, including reconstructing Civil War landscapes and identifying the ways that battlefields have changed over time. These reconstructions are especially important in dynamic coastal settings. The most interesting research he's conducted in his career occurred after he joined the research team studying the Confederate submarine H.L. Hunley. He is studying the sediments and microfossils from within the submarine hull to provide insights into the cause of sinking and exceptional taphonomic preservation of the crew.