For the evaluation of the internal water fluxes of wetlands and comprehension of their function within the hydrological cycle, the electrical resistivity tomography technique is a high-performance tool for the modeling of hydrodynamic environments, comprising data acquisition procedures based on transmission and reception sensors of electric potential fields as a result of predetermined configuration and the selection of arrays. The utilization of appropriate arrays is fundamental to obtaining data that truly represents the local geology, while an incorrect geometric configuration of electrodes might lead to failure to detect anomalies, impacting the comprehension of the dynamic processes. This research was conducted to make a comparative analysis of electrical resistivity tomography data acquired through Schlumberger, Wenner, and dipole-dipole arrays, which were supported by direct soil hydraulic conductivity data and vegetation analysis, allowing the correlation of surface infiltration zones and their continuity in-depth, making possible an evaluation of the array that best represents the study area in terms of soil, rock, and flux dynamics. The results revealed the Schlumberger array as the best electrode configuration for modeling, with the best correlation with direct surface data, which might be explained by the predominance of a horizontalized potential electric field flux, good signal-to-noise ratio, and discrimination capacity of vertical flux structures. Therefore, the results indicate the existence of a structure of water access and direct recharge for the regional aquifer (Tubarão aquifer system), characterized as a closed topographic depression located in a region of sugarcane farmimg.