Many National Wildlife Refuges (Refuges) have impaired water quality resulting from historic and current land uses, upstream sources, and aerial pollutant deposition. Competing duties limit the time available for Refuge staff to identify and evaluate potential water quality issues. As a result, water quality–related issues may not be resolved until a problem has already arisen. This study developed a geospatial approach for identifying and prioritizing water quality issues affecting natural resources (including migratory birds and federally listed species) within Refuge boundaries. We assessed the location and status of streams pursuant to the Clean Water Act in relation to individual Refuges in Oregon and Washington, United States. Although twelve Refuges in Oregon (60%) and eight Refuges in Washington (40%) were assessed under the Clean Water Act, only 12% and 3% of total Refuge stream lengths were assessed, respectively. Very few assessed Refuge streams were not designated as impaired (0% in Oregon, 1% in Washington). Despite the low proportions of stream lengths assessed, most Refuges in Oregon (70%) and Washington (65%) are located in watersheds with approved total maximum daily loads. We developed summaries of current water quality issues for individual Refuges and identified large gaps for Refuge-specific water quality data and habitat utilization by sensitive species. We conclude that monitoring is warranted on many Refuges to better characterize water quality under the Clean Water Act.