Water supply wells can act as conduits for vertical flow and contaminant migration between water-bearing strata under common hydrogeologic and well construction conditions. While recognized by some for decades, there is little published data on the magnitude of flows and extent of resulting water quality impacts. Consequently, the issue may not be acknowledged widely enough and the need for better management persists. This is especially true for unconsolidated alluvial groundwater basins that are hydrologically stressed by agricultural activities. Theoretical and practical considerations indicate that significant water volumes can migrate vertically through wells. The flow is often downward, with shallow groundwater, usually poorer in quality, migrating through conduit wells to degrade deeper water quality. Field data from locations in California, USA, are presented in combination with modeling results to illustrate both the prevalence of conditions conducive to intraborehole flow and the resulting impacts to water quality. Suggestions for management of planned wells include better enforcement of current regulations and more detailed consideration of hydrogeologic conditions during design and installation. A potentially greater management challenge is presented by the large number of existing wells. Monitoring for evidence of conduit flow and solute transport in areas of high well density is recommended to identify wells that pose greater risks to water quality. Conduit wells that are discovered may be addressed through approaches that include structural modification and changes in operations.