A stepwise logistic regression (LR) model was generated to evaluate the association between contamination of groundwater by nitrates with several risk factors such as soil types, farm facilities and practises, and well characteristics. The odds ratio was calculated to estimate the degree of impact that the associated variables had on the risk of contamination in a semiconfined multilayer aquifer underlying rural areas of Buenos Aires, Argentina. Duplicate farm groundwater samples (n = 160) were taken and nitrate was analyzed. Data, involving various farm factors, was gathered via two questionnaires concerning farm’s general and productive aspects, and well characteristics. Statistical tests were run between nitrates and each variable present in the survey. A 96.25% of the samples presented detectable nitrate levels, 40.91% of which had more than 45 ppm nitrates. The final LR model involved five of the variables under study: well age, soil permeability, depth of water table, location, and distance from well to contamination sources. Cross validation proved to be a good estimator of nitrate water contamination. Suspicions about how these characteristics influence groundwater contamination by nitrates were confirmed, and as these five factors represent a higher risk for this type of aquifer, their proper management may contribute to a better resource protection.