William A. McDonald was awarded the AIA Gold Medal for Distinguished Archaeological Achievement in 1981 in recognition of his role as a "pathfinder" who "pioneered in bringing about changes in the theory, methodology and general conduct of archaeological research in Greece." As the Director of the Minnesota Messenia Expedition, McDonald emphasized interdisciplinary rather than multidisciplinary collaboration among archaeologists, natural scientists, social scientists, and humanists. Concentrating his research efforts on the territory comprising the Late Bronze Age kingdom of Pylos, in 1953 McDonald undertook an archaeological survey of the 1,400 square mile region around the Palace of Nestor. From 1969-1975, he directed the excavation of Nichoria, a major Bronze and Iron Age settlement that was part of the Pylian kingdom.
In addition to his scholarly research, McDonald was also recognized for his dedication to teaching. He was member of the faculty of the Department of Classics at the University of Minnesota from 1948 to 1980, and was instrumental in founding the Honors Division of the College of Liberal Arts. He also helped to found the Center for Ancient Studies, an interdisciplinary graduate program. In 1973, the University presented him with its highest award, appointment as Regents' Professor of Classical Studies.
To honor his memory, his colleagues, students, and friends have established the William A. McDonald Lectureship in Aegean Prehistory as part of the National Lecture Program of the AIA. The McDonald Lecturer is selected annually by the Lecture Program Committee of the AIA.