The water supply of cities presents great challenges since the demand is concentrated in areas where human activities threaten water resources. Where available, deep confined aquifers are protected from contamination. But they often suffer from a lack of recharge and long term withdrawals shall be limited to protect the stock. In contrast, unconfined aquifers usually present greater recharge rates and may be of interest for drinking water supply. Though vulnerable to anthropogenic contamination, such aquifers often present a better quality than surface waters. This study discusses the relevance of using unconfined aquifers in urban areas and investigates the solutions to mitigate their vulnerability to contaminants. The approach is illustrated with a case study in the city of Bordeaux (France). Deep aquifers were subject to overpumping so that unconfined aquifers were considered as an alternative. A flow and transport groundwater model was implemented in a well field vulnerable to a contaminated stream. An adaptive, multi-objective optimization approach was proposed. The objective was to maximize the water production at the well field while minimizing stream water intrusion. The well-field operator can adjust production settings to optimum conditions in function of the observed stream water level and desired production rate. Such a smart use of unconfined aquifers may be advantageous in many cities around the world.