Household well water can be degraded by contaminants from the land's surface, but private well owners lack means to protect the source water from neighboring disturbances. Rural residents of southwestern Wisconsin, USA, rely on private well water, and the combination of land use and fractured carbonate bedrock makes groundwater vulnerable to contamination. To identify the extent, sources, and risk factors of private well contamination, randomly selected wells sampled during two-day periods in fall (n = 301) and spring (n = 529) were analyzed for nitrate and indicator bacteria, and a subset (n = 138) was sampled across four seasonal events for analysis of pathogens and microbial source tracking markers by quantitative polymerase chain reaction. Risk factors representing land use, hydrology, geology, and well construction were analyzed for associations with contamination in multivariable models. The importance of risk factors varied by contaminant, illustrating the multifaceted nature of rural groundwater quality. Nitrate contamination was associated with agricultural land use, and wells with casings that extended below a shale aquitard accessed less contaminated water than those drawing water from above it. Human fecal microbes were detected in 64 wells (46%), and rainfall was the key risk factor for contamination, indicating that wastewater from septic systems was available to contaminate wells when transport conditions were favorable. Manure microbes from cattle/ruminants and pigs were detected in 33 and 13 wells, respectively, and concentrations increased with the hectarage of cultivated land near wells. Pathogen genes for viruses, bacteria, and protozoa were detected in 66 wells (48%), including more detections of zoonotic than human-specific pathogens, and human Bacteroides, an indicator of wastewater, was an equivocal predictor of pathogen presence in private wells. Characterizing important elements of the setting, like geology, and identifying sources and risk factors for contaminants can inform landscape-level policies to protect groundwater quality.