Groundwater management needs detailed aquifer characterization, especially in semiarid costal aquifer systems that are under hydrological pressure. Our study area is in the Tordera delta, northeastern coast of Spain, where a detrital fluvio-deltaic aquifer system has been developed above granitic basement. The main purpose of this study is to characterize the complex lithological structure and the seawater intrusion state by combining hydrological information, audiomagnetotelluric (AMT) and seismic reflection and refraction models. This allowed us to provide spatially continuous information about aquifer properties and processes. Thus, we have determined the thickness and continuity of the aquifer units, as well as the morphology and depth to the basement. The models revealed that the main seawater intrusion main path is found in the western deltaic area that coincides with an existing buried paleochannel. This new result explains the anomalously high chlorine concentrations observed in the deep semiconfined aquifer more than 1,500 m inland.