The dataset includes names and geographic coordinates of gauge stations where flow and water quality (sediment, nitrogen, phosphorus) are measured in the Upper Mississippi River Watershed, Ohio River Basin, and Maumee River Basins. The data include estimates of risk indices (reliability, resilience, vulnerability) and a composite watershed health measure at gauge the stations, distributional properties of the indices, sensitivity to water quality standards, scale dependency of the indices, and statistical significance of the relationship between composite watershed health measure and land uses (agricultural, forested, and urban). This dataset is associated with the following publication: Ganeshchandra Mallya , G., M. Hantush, and R. Govindaraju. Composite measures of watershed health from a water quality perspective. JOURNAL OF ENVIRONMENTAL MANAGEMENT. Elsevier Science Ltd, New York, NY, USA, 214: 104-124, (2018).