His studies on the phosphorus cycle focused on nonpoint phosphorus pollution and how elevated phosphorus concentrations impacted the ecosystem of Lake Mendota. These investigations led Carpenter to devise strategies to manage the phosphorus cycle. By the mid-1990s he began to study the economics of eutrophication, in which he compared the benefits factories and farms receive by causing eutrophication to the benefits of keeping a lake clean and clear with the goal of maximizing the benefits on both sides. From 1999 to 2009 Carpenter led the North Temperate Lakes Long Term Ecological Research at UW-Madison. In 2009 he became director of the UW-Madison Center for Limnology. In 2017 he retired as director in order to pursue research interests. Carpenter is Chair of the Science Committee for the Program on Ecosystem Change and Society of the "Future Earth. He is co-Editor in Chief of the journal "Ecosystems", and a member of governing boards for the Stockholm Resilience Centre. In 2000-2005 he was co-chair of the Scenarios Working Group of the Millennium Ecosystem Assessment. He led the North Temperate Lakes research site of the Long Term Ecological Research Network program at the University of Wisconsin in 1999-2009. He is a former President of the Ecological Society of America. As of 2011, Carpenter has published 5 books and about 450 scientific papers, book chapters, reviewed reports and commentaries. Carpenter is the 2011 laureate of the Stockholm Water Prize for his research on how lake ecosystems are affected by their surrounding landscape and by human activities such as nutrient loading, fishing, and introductions of exotic species. His other awards include a Pew Fellowship in Conservation and Environment, the Naumann-Thienemann medal of the International Society of Limnology in 2007 for "research that has built bridges between ecological theory, ecosystem experiments, and management of complex limnological problems" and the work that "has elucidated the importance of the trophic cascade and regime shifts in the management of lakes", the G. Evelyn Hutchinson Award in 1999 from the American Society of Limnology and Oceanography, the Robert H. MacArthur Award in 2000 from the Ecological Society of America, the Excellence in Ecology Prize (ECI Prize) in 2000 from the Ecology Institute for limnetic ecology, and the Ramon Margalef Prize in Ecology in 2018  from the Generalitat de Catalunya. Carpenter has also been awarded membership in the US National Academy of Sciences and Foreign Membership of the Royal Swedish Academy of Sciences.