Implementation of an order by the International Joint Commission in January 2000 has changed operating procedures for dams that regulate two large reservoirs in Voyageurs National Park in northern Minnesota. These new procedures were expected to restore a more natural water regime and affect water levels, water quality, and trophic status. Results of laboratory analyses and field measurements of chemical and physical properties from May 2001 through September 2003 were compared to similar data collected prior to the change in operating procedures. Rank sum tests showed significant decreases in chlorophyll-a concentrations and trophic state indices for Kabetogama Lake (p=0.021) and Black Bay (p=0.007). There were no significant decreases in total phosphorus concentration, however, perhaps due to internal cycling of phosphorus. No sites had significant trends in seasonal total phosphorus concentrations, with the exception of May samples from Sand Point Lake, which had a significant decreasing trend (tau=-0.056, probability=0.03). May chlorophyll-a concentrations for Kabetogama Lake showed a significant decreasing trend (tau=-0.42, probability=0.05). Based on mean chlorophyll trophic-state indices (2001-03), Sand Point, Namakan, and Rainy Lakes would be classified oligotrophic to mesotrophic, and Kabetogama Lake and Rainy Lake at Black Bay would be classified as mesotrophic. The classification of Sand Point, Namakan, and Rainy Lakes remain the same for data collected prior to the change in operating procedures. In contrast, the trophic classification of Kabetogama Lake and Rainy Lake at Black Bay has changed from eutrophic to mesotrophic.