Alluvial aquifers are important sources of drinking water for Eastern Iowans. However, alluvial aquifers are particularly susceptible to contamination from surface activities due to their shallow depth, permeable material, and close connection to surface waters. Domestic wells and monitoring wells located in alluvial aquifers within the Eastern Iowa Basins study unit, which covers 19,500 square miles, were sampled. The study unit includes the Wapsipinicon, Cedar, Iowa, and Skunk River basins, all of which drain to the Mississippi River. During the summer of 2017, a sampling effort of twelve domestic, twenty-four monitoring, and two municipal wells within the Eastern Iowa Basins study unit was conducted. Water quality data, including dissolved oxygen, nitrate, ammonia, dissolved organic carbon, iron, and sulfate concentrations, was collected. Additionally, microbial DNA samples were collected via filtration of alluvial groundwater. We tested the hypotheses that microbial species richness would decrease with increasing NO3--N concentrations and that differences in groundwater chemistry would be associated with differences in microbial community taxonomy. Overall, the current state of microbial populations in alluvial aquifers was studied, where the risk of groundwater contamination is high.