Lee is one of the founders of the environmental justice movement. Lee is best known for his principal authorship of the 1987 report Toxic Wastes & Race in the United States through the United Church of Christ. Lee is also well known for his work in establishing the US Environmental Protection Agency's (EPA) Office of Environmental Justice and the National Environmental Justice Advisory council. In the 1970s, Lee worked as a shop steward with a hospital workers union. In 1994, Lee worked on Executive Order 12898 on environmental justice.

Lee is currently the Senior Policy Advisor in the Office of Environmental Justice at the EPA and previously was the Director. Before working at the Office of Environmental Justice, Lee was the Environmental Justice Program Director of the United Church of Christ. Lee has served on many boards and committees, such as the EPA National Environmental Justice Advisory Council, the EPA Children's Health Protection Advisory Committee, and the Institute of Medicine Committee on Environmental Justice.