Lee's research focuses on Mars, asteroids, and impact craters, in particular in connection with the history of water on planets and the possibility of extraterrestrial life. He is known internationally for his work on Moon and Mars analogs in the Arctic, Antarctica, and other extreme environments on Earth. He is the author and co-author of over 100 scientific publications, and first proposed the "Mars Always Cold, Sometimes Wet" model of Mars evolution based on field studies of the geology of Earth's polar regions.