In 1991, the U.S. Geological Survey (USGS) began a study of more than 50 major river basins across the Nation as part of the National Water-Quality Assessment (NAWQA) project of the National Water Quality Program. One of the major goals of the NAWQA project is to determine how water quality and ecological conditions change over time. To support that goal, long-term consistent and comparable ecological monitoring has been conducted on streams and rivers throughout the Nation. Fish, invertebrate, and algae data collected as part of the NAWQA program were retrieved from the USGS Aquatic Bioassessment database for use in trend analysis. Ultimately, these data will provide insight into how natural features and human activities have contributed to changes in ecological condition over time in the Nation’s streams and rivers. This dataset is a model archive containing all input files and R source code to reproduce the results of the ecological trend analysis described in the associated U.S. Geological Survey Scientific Investigations Report. Associated output files are also included in the archive. Data preparation for input to the model is fully described in the above mentioned report.