In 1951, the Faculty of Fisheries for maritime and inland fisheries was established at the Tertiary College of Agriculture that was functioning in Olsztyn at that time. During the fifties and sixties, the Faculty enjoyed full academic rights, the best scientific staff in Poland in the field of fisheries, and offered a program of education for students of Fisheries Science.

The best known professors of that Faculty were Stanisław Korwin-Sakowicz, the first Dean and the director of the Institute of Inland Fisheries, and Przemysław Olszewski, Dean of the Division of Inland Fisheries and founder of the Faculty of Water Protection and Inland Fisheries. Also well-known were Robert Towarnicki, Eugeniusz Grabda, Franciszek Pliszka, Stanisław Bernatowicz, Bolesław Dąbrowski, Józef Mikulski, Walerian Cięglewicz, Kazimierz Stegman, Władysław Mańkowski, Józef Popiel, Teofil Dąbrowski, Marian Zięcik, among others.

During the years 1966-1968, the chairs specializing in maritime subjects were moved to the Tertiary College of Agriculture in Szczecin, where the Faculty of Maritime Fisheries and Food Technology was established. The four Chairs left in Olsztyn (Fisheries, Limnology, Ichthyology and Economies of Fishery Enterprises) were used to establish the Division of Inland Fisheries at the Faculty of Animal Husbandry. In 1970, on the initiative of Professor Przemysław Olszewski and the scientific personnel, the Faculty of Water Protection and Inland Fisheries was established by the executive regulation of the Ministry of Education and Tertiary Education, with the support of the Ministry of Environmental Protection and Natural Resources. This new faculty incorporated the assets of the Division of Inland Fisheries and the Chair of Zoology from the Faculty of Animal Husbandry.

The first Dean of this new Faculty was Assistant Professor, dr. hab. Tadeusz Wojno, later Professor and Deputy Rector of the Tertiary College of Agriculture. He was followed in the office by Professors Tadeusz Januszkiewicz, Zofia Różańska, Maria Brylińska, Konstanty Lossow (twice), Andrzej Mamcarz, Janusz Guziur, Irena Wojnowska-Baryła (twice), Krystyna Demska-Zakęś, Mirosław Krzemieniewski (twice).

During the years 1970-1996, the organizational structure of the Faculty changed to reflect the continually updated curriculum and specialties for graduates. Until 1996, the Faculty consisted of five Departments: Fisheries, Basic Fishery Sciences, Zoology, Ecology, and Chemistry and Technology of Water and Wastewater. Since then, multiple changes to the Departments in the Faculty have been made to comply with external requirements and the needs of the students and local area. As of January 31, 1997, the Faculty changed its name to the Faculty of Environmental Sciences and Fisheries.

According to the decision by the Central Commission for Scientific Titles and Scientific Degrees in Warsaw on July 5, 1999, the Council of the Faculty of Environmental Sciences was given the rights to grant the degree of doctor habilitatus in agricultural sciences. After this, changes continued to be made in the structure and content of the courses in environmental protection to reflect changes in the local economy and environment.

In 2011, the Faculty began to teach students with a specialization in Tourism and Recreation, in addition to those with specializations in Environmental Protection, Environmental Engineering, and Fisheries.

On May 1, 2012, the Faculty was renamed again to become the Faculty of Environmental Sciences, which corresponds to its current profile in education and research.