Seasonal variability in groundwater pumping is common in many places, but resulting effects of seasonal pumping stress on the quality of water produced by public-supply wells are not thoroughly understood. Analysis of historical water-quality samples from public-supply wells completed in deep basin-fill aquifers in Modesto, California (134 wells) and Albuquerque, New Mexico (95 wells) indicates that several wells have seasonal variability in concentrations of contaminants of concern. In Modesto, supply wells are more likely to produce younger groundwater with higher nitrate and uranium concentrations during the summer (high) pumping season than during the winter (low) pumping season. In Albuquerque, supply wells are more likely to produce older groundwater with higher arsenic concentrations during the winter pumping season than during the summer pumping season. Seasonal variability in contaminant concentrations in Modesto is influenced primarily by effects of summer pumping on vertical hydraulic gradients that drive migration of shallow groundwater through the aquifer to supply wells. Variability in Albuquerque is influenced primarily by the period of time that a supply well is idle, allowing its wellbore to act as a conduit for vertical groundwater flow and contaminant migration. However, both processes are observed in each study area. Similar findings would appear to be likely in other alluvial basins with stratified water quality and substantial vertical head gradients. Results suggest that even in aquifers dominated by old groundwater, changes to seasonal pumping patterns and/or to depth of well completion can help reduce vulnerability to selected contaminants of either natural or anthropogenic origin.