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• We separate the roles of upward discharge and aquitards in flowing artesian zone. • Basinal flow are coupled with well hydraulics to examine hydraulics of flowing wells. • A low K aquitard causes a large flowing artesian zone but low stable discharge rate. • Baseflow reduction is the main source of groundwater derived in flowing wells. Causes and water sources of flowing artesian wells attracted the interest of many hydrogeologists throughout history, however, a quantitative model that satisfactorily considers the roles of topography, groundwater recharge/discharge and aquitards on hydraulics of flowing wells is still lacking. In this study, a three-layer river-valley basin with a recharge boundary is used to obtain the basinal flow field, spatial distribution and transient discharge rates of flowing wells. Even if there is an aquitard separating the unconfined and the confined aquifers, groundwater discharge to the river still plays a critical role in occurrence of flowing wells. An aquitard with lower permeability would enlarge the zone with flowing wells, implying that flowing wells are more likely to occur in basins with continuous aquitards. By comparing flowpaths and inter-aquifer leakages before and after numerically installing a flowing well in a three-layer basin, we find decreased upward leakage in the discharge limb plays a much larger role than increased downward leakage in the recharge limb in the stable discharge rate of a flowing well. This recognition is different from previous studies where the stable discharge rate is supported only by downward leakage from the overlying aquifer. By considering well hydraulics in a basinal background flow field, this study improves understanding of the mechanisms of flowing artesian wells and the interaction of surface water and deep groundwater, indicating that flowing wells are valuable for sampling deep groundwater representative of deep and old groundwater in the discharge area of a basin. [ABSTRACT FROM AUTHOR]