National Wildlife Refuges may have impaired water quality resulting from historic and current land uses, upstream sources, and aerial pollutant deposition. National Wildlife Refuge staff have limited time available 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. The National Wildlife Refuge System Water Quality Information System (WQIS) is a relational database developed for use by U.S. Fish and Wildlife Service staff to identify existing water quality issues on refuges in the United States. The WQIS database relies on a geospatial overlay analysis of data layers for ownership, streams and water quality. The WQIS provides summary statistics of 303(d) impaired waters and total maximum daily loads for the National Wildlife Refuge System at the national, regional, and refuge level. The WQIS allows U.S. Fish and Wildlife Service staff to be proactive in addressing water quality issues by identifying and understanding the current extent and nature of 303(d) impaired waters and subsequent total maximum daily loads. Water quality data are updated bi-annually, making it necessary to refresh the WQIS to maintain up-to-date information. This manual outlines the steps necessary to update the data and reports in the WQIS.