Gene Elden Likens (born January 6, 1935) is an American limnologist and ecologist. He co-founded the Hubbard Brook Ecosystem Study at the Hubbard Brook Experimental Forest in 1963, and founded the Cary Institute of Ecosystem Studies in Millbrook, New York in 1983.

A leading pioneer in long-term multidisciplinary ecological studies, Likens examines energy flow and biogeochemical flux models in the ecosystems of forests, streams and lakes. Likens is best known for leading the team of scientists that discovered acid rain in North America, and connected fossil fuels with increasing acidity of precipitation. In addition to its scientific impact, this work has influenced public debate and governmental policy, particularly the United States Congress's Clean Air Act Amendments of 1990.

Gene Likens was born in Pierceton, Indiana. Likens received his B.S. in zoology at Manchester University (North Manchester, Indiana) in 1957, followed by his M.S. in zoology in 1959 from the University of Wisconsin–Madison. He received his Ph.D. in zoology in 1962, also from the University of Wisconsin–Madison, for his thesis on Transport of radioisotopes in lakes.

Likens was an instructor and associate professor at Dartmouth College from 1963 to 1969. In the 1960s, Likens did early work in the dry valleys of Antarctica, examining the thermal structures of Lake Vanda and Lake Bonney.

Likens was co-founder in 1963 of a group with F. Herbert Bormann, Robert S. Pierce and Noye M. Johnson working on the Hubbard Brook Ecosystem Study at the Hubbard Brook Experimental Forest in the White Mountains of New Hampshire. The study immediately found that the rain was abnormally acidic, and the group carried out one of the first scientific studies linking acid rain to air pollution such as sulphur dioxide from the use of fossil fuels.

In 1988, Hubbard Brook was designated by the National Science Foundation as an LTER, a site for collaborative long term ecological research. In 2005, Hubbard Brook celebrated 50 years of research at the site. Likens' work in the area is considered "one of the world’s most comprehensive studies on how air pollution and land use shape forested watersheds". Work at Mirror Lake, at the lower end of the Hubbard Brook Valley, has been particularly important in understanding the importance of physical, chemical, and biological linkages involving the lake and its watershed and airshed. Liken has extensively studied biogeochemical cycles describing the flow of matter within ecosystems. Riparian zones linking water and land are particularly important in maintaining the health of wild lands. Liken has also done important work on deforestation and its potential impact on the chemistry of watersheds. This research has had significant impacts on programs for forest management, in particular the United States Forest Service's adoption of a 100–year rotation policy.

Likens and others devised a range of highly influential long-term experiments on an ecosystemic scale. These include the small-watershed model of nutrient cycling, in which all water entering and leaving a naturally-bounded watershed is measured, enabling scientists to calculate the hydrologic budget of the watershed. This model has been "extremely influential" in the examination of ecosystems, and is central to the examination of urban ecosystems such as Baltimore. Likens' work is considered "classic", and he is credited with establishing a "guiding paradigm" for other ecologists.

In 1969, Likens joined the faculty of Cornell University. He served as an associate professor from 1969 to 1972, and as a full professor from 1972 to 1983. In addition to being a professor of ecology in the Section of Ecology and Systematics (later named the Department of Ecology & Evolutionary Biology), he served as its acting chairman (1973-1974) and chairman (1982-1983). In January 1983 he was named Cornell University's Charles A. Alexander Professor of Biological Sciences. While at Cornell University, he served as chairman of the Section of Ecology and Systematics.