In this research, a hydraulic characterization of a 14 km segment of the San Pedro River, flowing through the center of the Aguascalientes Valley, was conducted. More than 50 years of flow measurement records were processed to obtain daily flows during dry and rainy seasons. Through geospatial analysis, areas with hydraulic retention, influenced by the region’s topography and sediment accumulation during the flood season, were identified. Similarly, the digital map of geological surface features revealed that some of these structures spatially coincide with these retention areas. Later, potential hydraulic connectivity between the surface and the aquifer were evaluated in the identified hydraulic stagnation areas (HSAs) using vertical electrical soundings (VESs). Finally, through an experimental process in which water collected from the San Pedro River flowed through a device filled with surface soil taken from the retention areas, the potential retention of pollutants by the local soil was evaluated based on toxicity tests using the monogonont rotifer Lecane papuana. The findings suggest the presence of three hydraulic stagnation areas (HSAs) in the examined section of the river, with one of them intersected by a surface discontinuity. According to the results of the VES, the water table beneath the HSA varies between 70 and 90 m in depth. Further analysis of the vertical electrical sounding (VES) results suggests the presence of vertical hydraulic connectivity between the San Pedro River and the local aquifer in the hydraulic stagnation areas (HSA). This is indicated by the identification of low-resistivity strata associated with highly saturated soil above the water table, as measured in the adjacent pumping wells. Additionally, the experiments involving the device filled with soil showed a reduction in water toxicity (ranging from 12 to 40%) as the San Pedro River water flowed through a 1 m column of local near-surface soil. The results of this experimental work suggest that the soil acts as a natural filter for contaminant transport under conditions in time and space similar to those of the experiment. However, there is still a significant research niche in conducting an experimental campaign in terms of hydrogeochemistry to obtain more specific results.