The Montana State Board of Health was established in 1901. The Division of Water and Sewage was created in 1911. Its first director was W. M. Cobleigh. From the organization of the division until 1923, bacteriological and chemical examinations of water samples were carried on at the State Agricultural College in Bozeman. On July 1, 1923, the office and laboratory were moved to Helena and H. B. Foote became the division director. W. M. Cobleigh continued as a consultant. In the early years, work centered around installation of sewage treating plants to prevent pollution of streams, protect watersheds, and provide clean drinking water; creation of regulations governing preparation and submission of designs for sewer systems and treatment plants; and analyzing public and private water supplies. The division also analyzed water from swimming pools and reviewed heating, lighting, ventilating, and plumbing plans for new school buildings to insure a safe environment.

During the Great Depression of the 1930s, the work of the Water and Sewage Division increased markedly because of the need to examine water supplies used in Civilian Conservation Corps (CCC) camps and resettlement projects. Also during this period, the State Board of Health cooperated with the United States Public Health Service and the Work Projects Administration (WPA) in sponsoring the Montana Community Sanitation Program. The program was designed to eliminate insanitary devices by the construction of sanitary privies on public and private property wherever sewer systems were impracticable for any reason. On April 15, 1944, the division was renamed by the State Board of Health the division of Sanitary Engineering because of the expansion of field work being done by the division and the development of sanitary engineering as a more clearly-defined field.

By 1944, the division was conducting field inspections of sewage disposal systems, stream pollution problems, and public swimming pools. The division also reviewed plans for public water supplies, public sewage and industrial waste disposal systems, and public swimming pools. Included in the studies of stream pollution problems was the mine and smelter wastes in the upper reaches of the Clark Fork River. The 1950-1952 biennium opened with a large number of staff vacancies, including the division director of the Sanitary Engineering Division. In May 1950, the State Board of Health and the State Board of Examiners reached a general agreement on the subject of adequate salaries for staff members of the State Board of Health. This general agreement served as the basis for initiating a department-wide reorganization.

As part of the reorganization, the Division of Sanitary Engineering and the Division of Food and Drug were combined to create a new Division of Environmental Sanitation. C. W. Brinck was appointed director of the new division on May 1, 1951. The new division was divided into three sections: water, sewage, and general sanitation. The Water Section was in charge of water supplies-- both public and private swimming pools, well drilling for public water supplies, and review of plans for waterworks, swimming pools, school buildings, and other public buildings. The Sewage Section was in charge of sewage disposal, stream pollution abatement, plan review, sewage plant systems, cesspool and septic tank cleaning, and garbage disposal. The General Sanitation Section was itself divided into two areas run by the sanitarian and by the chemist. Sanitary inspection services included inspections of restaurants, meat markets, food manufacturing, soft drink/ice cream parlors, tourist camps, locker plants, camp sanitation, and mattress factories. The chemist was in charge of the laboratory, which conducted analyzes of water, sewage, soft drinks, meats, bakery products, canned goods, fruits for spray residue, insecticides and other poisons, drugs, and liquors.

In 1967, the Legislative Assembly created the State Department of Health. The State Board of Health continued in an advisory capacity, but the day-to-day administration of the state laws regarding public health and related matters was delegated to the new department. In 1971 the State Department of Health was abolished and replaced by a new Department of Health and Environmental Sciences. The State Board of Health continued as an advisory board, but was renamed the Board of Health and Environmental Sciences.

The Environmental Sciences Division eventually became its own separate department, renamed the Department of Environmental Quality (DEQ), in 1995, comprised of the following divisions: Director’s Office, Air Quality, Centralized Services, Energy, Environmental Remediation, Reclamation, Waste Management, and Water Quality. The mission of the Water Quality Bureau (now Water Quality Division) is to assure that water quality is maintained and improved so that state waters can support all their beneficial uses. The goal being to work with the public, agencies, and other interests to evaluate, maintain, and improve the quality of state waters.