The Nebraska Water Quality Index, under development by the Nebraska Department of Environment and Energy, summarizes in a single value eight environmental parameters that have been regularly monitored in Nebraska for nearly 20 years. The water quality parameters used in the Nebraska Water Quality Index have been shown in previous studies to be critical to bacterial growth. As such, this index has the potential to correlate with the microbial community in freshwater systems. Here, I relate the Nebraska Water Quality Index to lotic microbiome composition and structure using 16S rRNA gene amplicon sequence data collected from the North Platte River Basin, Nebraska. Gini-Simpson alpha diversity was significantly negatively correlated with Nebraska Water Quality Index ratings, as were the relative abundances of several bacterial orders: Absconditabacteriales, Burkholderiales, Campylobacterales,Oscillospirales,?Rhizobiales, and Vicinamibacteria Subgroup 17. Nebraska Water Quality Index ratings were positively correlated with Flavobacteriales and Saccharimonadales. Analysis of environmental parameters suggested that total nitrogen played a substantial role in shaping the microbial community and water quality. The Nebraska Water Quality Index is a convenient method of summarizing the physiochemical parameters of a stream environment to monitor spatiotemporal trends in water quality and gauge the success of ecosystem restoration efforts. Analysis of the aquatic microbial community in conjunction with the Nebraska Water Quality Index may help identify the cause of water quality problems. For instance, Oscillospirales is associated with fresh cattle manure. The presence of Oscillospirales in areas of low Nebraska Water Quality Index Ratings could help users identify sources of cattle manure pollution