NAMC was created in 1992 as a partnership between the Department of Fisheries and Wildlife at Utah State University (USU), the US Forest Service (USFS), and the US Bureau of Land Management (BLM). Dr. Jeff Kershner (USFS stationed at USU) and Dr. Charles Hawkins (USU faculty) proposed the creation of NAMC as a way that USU, the USFS, and BLM aquatic scientists could collaborate to enhance the development and application of biological monitoring and assessment programs on public lands. Mark Vinson, a BLM aquatic ecologist, served as its first Director starting in 1992. NAMC initially focused on processing aquatic invertebrate samples collected by USFS and BLM staff who used data from these samples to inform local project management. Vinson started the development of a database to manage the rapidly increasing amount of biological monitoring data that the USFS and BLM were producing each year. That database now consists of almost 70 million individual invertebrates identified from more than 104,000 samples taken at almost 42,000 sites. These data include 2.7 million occurrence records for 6122 different taxa and are used by NAMC staff to address both basic and applied research questions regarding the distribution of both individual species and entire assemblages. Following Vinson’s departure in 2009, the BLM hired Scott Miller to serve as NAMC Director. From 2009 to 2020, he increased staffing within NAMC; led the development of BLM’s nationwide Lotic Assessment, Inventory, and Monitoring Strategy; and promoted the implementation of best monitoring practices across BLM lands.

Between 2005 and 2020, the Department of Watershed Sciences also hosted a second, sister center (the Western Center for Monitoring and Assessment of Freshwater Ecosystems – aka the WMC) with initial funding from the US Environmental Protection Agency to Hawkins. The mission of the WMC was to assist state, tribal, and federal water quality agencies in developing scientifically sound bioassessment programs. Much of the WMC’s work focused on advancing the theory and application of two main elements common to all bioassessment programs: (1) the characterization and application of benchmarks (reference conditions) needed to distinguish the effects of human disturbance from that of natural environmental variability on measures of the biological, chemical, and physical condition of aquatic ecosystems and (2) development and refinement of numerical indices used to measure ecological status. This work later involved additional collaborations with the US Geological Survey and the National Park Service in addition to continuing collaborations with the USEPA, USFS, and BLM. During this time, the WMC collaborated extensively with NAMC on many projects including the refinement of the NAMC database.

In 2020, NAMC and the WMC were merged (as NAMC) with Charles Hawkins currently serving as Director.