In the test site of Castellana Grotte (Southern Italy), since 2016, around 2300 m3d−1 of tertiary treated wastewater has been alternatively spread in nine infiltration trenches, dug into fractured and karstified limestone. In one of these trenches, located upstream, seasonal variations in the infiltration rate were observed, with a lower infiltration rate during summer than in winter. This effect could be due to the occurrence of a bioclogging phenomenon in the warm season. In addition, time-lapse electrical resistivity tomography (ERT) was carried out in two different periods, corresponding to the wet and dry seasons, in order to investigate the infiltration process dynamics below the bottom of the trench. Remarkable variability was observed between the south and north sides of the trench—clearly related to the local-scale heterogeneity of the rock formation of the trenches. The results suggest that such an integrated approach should be considered of great interest in case of using infiltration trenches as managed aquifer recharge (MAR) plants. This methodology could provide useful information about the heterogeneities of the rock formation, supporting an alert system for the identification of clogging effects during the life cycle of the plant.