The Bureau of Ocean Energy Management (BOEM) regulates offshore energy development on the Outer Continental Shelf (OCS) of the United States. As part of the environmental review process of permitted industry activities, BOEM requires oil and gas operators to conduct an archaeological and benthic biological geophysical survey and, if necessary, remotely operated vehicle or diver investigations in their areas of operation. We therefore have detailed archaeological data of deep waters of the Gulf of Mexico at a scale much greater than anywhere else in the world. These surveys have identified well over 100 shipwrecks in deep water. In the last couple of decades, BOEM has funded or supported multidisciplinary research on many of these deep-water shipwrecks. Recently, BOEM scientists have designed research projects that treat archaeology, biology, and geochemistry as equal with regard to project goals. By integrating research efforts, new insights and discoveries have been made, for example with regard to biological community structure relative to archaeological material properties and mutual site formation. This chapter synthesizes the evolution of several of these research endeavors and the discoveries that could only have been achieved through this type of integrated multidisciplinary research.