Studying the relationship between river water and shallow groundwater (SGW) during flood events is a research topic receiving increasing attention for many reasons. This phenomenon was studied with respect to Mohács Island of the Danube (Hungary) in an area protected by a levee. Floods only infiltrate into the island through the aquifer, where production wells for drinking water supply are located. Our objective was to reveal how the Danube and water abstraction from production wells control groundwater levels in the observation wells, and we also studied the effect of the precipitation events and the lag times of the influencing variables compared to the peak of groundwater waves in observation wells. The effects of these factors were summarized by a linear regression model (LM) with lag times. We developed an application because we had time-series for thirty groundwater wells and five major flood events of the Danube. Kriging was used to generate impact maps of the Danube and production wells. A propagation map of the Danube flood wave into the groundwater aquifer was also generated. We used geological information to explain the findings that the river flood waves propagate with the same wavelength and decreasing amplitude in the covered aquifer and with an elongated wavelength in uncovered conditions.