Although many U.S. homes rely on private wells, few studies have investigated the quality of these water sources. This cross-sectional study evaluated private well water quality in Maryland, and explored possible environmental sources that could impact water quality. Well water samples (n = 118) were collected in four Maryland counties and were analyzed for microbiological and chemical contaminants. Data from the U.S. Census of Agriculture were used to evaluate associations between the presence of animal feeding operations and well water quality at the zip code level using logistic regression. Overall, 43.2% of tested wells did not meet at least one federal health-based drinking water standard. Total coliforms, fecal coliforms, enterococci, and Escherichia coli were detected in 25.4%, 15.3%, 5.1%, and 3.4% of tested wells, respectively. Approximately 26%, 3.4%, and <1% of wells did not meet standards for pH, nitrate-N, and total dissolved solids, respectively. There were no statistically significant associations between the presence of cattle, dairy, broiler, turkey, or aquaculture operations and the detection of fecal indicator bacteria in tested wells. In conclusion, nearly half of tested wells did not meet federal health-based drinking water standards, and additional research is needed to evaluate factors that impact well water quality. However, homeowner education on well water testing and well maintenance could be important for public health.