The Department of Natural Resources was created in September 1991 as a result of a merger between the Department of Mines and Energy and the Department of Lands and Forests. An extensive strategic planning process started in July 1992 and culminated in a major departmental reorganization in March 1995. Smaller reorganizations also occurred in March 1996, with the creation of the Resources Corporate Services Unit for financial, human resources and information technology services, and in November 1996, with the remaining other central services transferred within the Department.

In 1998, the Protected Areas program was transferred to the Department of the Environment, and the Petroleum Directorate became a standalone agency reporting to the Minister of Economic Development and Tourism. In June 2002 the Department's energy related responsiblilities were transferred to the Department of Energy.

The resources of the department are organized into four branches;

• Renewable Resources
• Regional Services
• Mineral Resources
• Land Services
• and a Planning Secretariat.

The Resources Corporate Services Unit (RCSU) provides financial, human resources and information technology related services.