Water‐level increase after rainfall is usually indicative of rainfall recharge to groundwater. This, however, may not be true if the Lisse effect occurs. This effect represents the water‐level increase in a well driven by airflow induced by an advancing wetting front during highly intensive rains. The rainwater, which may behave like a low‐permeability lid, seals the ground surface so that the air pressure beneath the wetting front is increased because of air compression due to downward movement of the wetting front. A rapid and substantial rise of the water level in the well screened below water table, which bears no relationship to groundwater recharge, can be induced when various factors such as soil properties and the rain‐runoff condition combine favorably. A transient, three‐dimensional and variably saturated flow model was employed to study the air and groundwater flows in the soil under rain conditions. The objectives of this paper are two‐fold: to evaluate the reliability of the theory of the Lisse effect presented by Weeks to predict its magnitude in modeled situations that mimic the physical complexity of real aquifers, and to conduct parametric studies on the sensitivity of the water‐level rise in the well to soil properties and the rain event. The simulation results reveal that the magnitude of the Lisse effect increases with the ponding depth. Soil permeability plays a key role in generating the Lisse effect. The water‐level rise in the well is delayed relative to the air‐pressure rise in the unsaturated zone when the soil permeability is low, and the maximum water‐level rise is less than the maximum air pressure induced by rain infiltration. The simulation also explores the sensitivity of the Lisse effect to the van Genuchten parameters and the water table depth.