The University of the Aegean was founded in 1984, along with its School of Social Sciences. The Department of “Natural Environmental Sciences”, initially part of the School of Social Sciences, was one of the first departments of the University. Its first doctoral candidate graduate students were accepted in the academic year 1986-1987 and its first undergraduate students in the academic year 1987-1988. In 1989, the Department was renamed the “Department of Environment”.  In January 2004, it was moved from the School of Social Sciences to the newly established School of Environment along with the Department of Marine Sciences.

The Department of Environment operates a four-year undergraduate program and three graduate programs which offer Master of Science (M.Sc.) degrees and Doctor of Philosophy (Ph.D.) degrees in Environmental Science.