In September of 1988, he joined the faculty in the Department of Geography at the University of Wisconsin-Madison where he taught cartography and GIS and helped establish a GIS program. In January of 1994, Lynn returned to UGA where he teaches GIS and has helped establish certificate programs in GIS at both the undergraduate and graduate levels. In May of 1999, Lynn assumed a Research Geographer position with the USGS in addition to his academic job at UGA.
He is currently involved in research in geographic information science, with publications on theoretical aspects of geographic representation, human cognition of geographic phenomena, automatic feature extraction from images, and visualization, and applications of geographic information science to precision farming, watershed modeling, and water quality. Other current work includes research toward a multidimensional theory of geographic phenomena, multiple representations, map projections, and autostereoscopic visualization.