•Seawater intruded about 2 km in the coastal region, affecting water resources.•The Taylor diagram indicated that L1 robust is the best inversion method.•The new uncertainty approach indicated a considerable variation in seawater intrusion extent.•The BERT reached lower RMS error in less iteration compared to RES2DINV.•Mesh size did not improve the inversion results significantly. Seawater intrusion (SWI) is one of the most important phenomena which occurs in shorelines and islands and affects groundwater storage in the region. This study aims to investigate how far seawater has intruded in a coastal area and what is its extent variation. The results can lead to different management plans. To achieve these goals, a geoelectrical method is applied in the coastal aquifer of Chaouia, Morocco. In order to choose the best inversion process, different settings are applied in two different software packages namely RES2DINV and BERT and the results are compared using the Taylor diagram. Also, to determine the minimum and maximum SWI extent in the region, a new approach of uncertainty analysis is applied in the inversion process by the Monte Carlo method. The general results indicate that the seawater has intruded about 2 km into the shore. The obtained results show that by considering uncertainty, there is a sensible difference between the maximum and minimum extent of SWI (maximum 9% variation in the area of SWI) which should be noted when doing water research management studies. The methodology procedure in this study can be applied to different coastal areas around the world.