William McCoy's primary research concerns Quaternary geomorphology and stratigraphy. He has worked on the chronology of alpine glaciation and lake-level changes in the western United States. Much of the lake-level work focused on the application of aminostratigraphic methods to Quaternary deposits of closed-basin lakes. That work resulted in an aminostratigraphic framework for the exposed records of Lakes Bonneville and Lahontan. Research has also been conducted on the determination of Quaternary paleotemperatures (based on rates of isoleucine epimerization in fossil mollusk shells) in the Great Basin and the investigation of the paleoclimates and paleohydrology that supported the greatly expanded Pleistocene glaciers and lakes of that region. Recently he has been involved in research projects concerning the aminostratigraphy of Pleistocene loess deposits of the midwestern U.S., China, and central Europe. In collaboration with Eric A. Oches, an aminostratigraphic framework has been developed for a region including the Czech Republic, Slovakia, Hungary, and Austria. Most recently, work is being conducted on loess aminostratigraphy and paleothermometry across Europe from Belgium to Ukraine, including Germany, Czech Republic, Austria, Hungary, Serbia, and Romania.