The expansion of feedlot activities in the NW zone of Buenos Aires Province (Argentina) has increased the risk of groundwater contamination, due to a higher concentration of manure on the soil surface. Groundwater is shallow and the soils are sandy loam, which are factors that make this area vulnerable to pollution. The heterogeneous distribution of manure in the pens and the hard compacted layers in the soils makes it difficult to make a representative soil and groundwater sampling. The purpose of this work was the use of electrical resistivity tomography (ERT) to aid subsequent sampling campaign for the delineation of the spatial distribution of nitrates, in soils and groundwater at pens of a feedlot, with different times of animal confinement. The soil sampling, up to 3 m depth was performed taking into account the anomalies of bulk resistivity. The sites of lower resistivity than background values were potentially associated with different levels of soil salinization. Volumetric water content and concentration of N–NO3− of the soils were determined. The electrical resistivity sections indicated low values in the saturated and unsaturated zone, near waterers and feedbunks and a decrease in the sense of decreasing topography. This reduction was also observed at sites of higher water content, in Pen 1 (4 months of animal confinement) associated with the proximity of the water table. The values of N–NO3− contents were much higher at Pen 2 (7 years of confinement) with values between 436 and 877 kg N–NO3 ha−1, while at Pen 1 the range was from 43 to 129 kg N–NO3− ha−1. At both pens, the lower resistivity was associated with sites of higher contents of water and N–NO3−. The presence of an impermeable hard soil layer, below the surface of Pen 1, enhanced superficial runoff toward the lower zone outside the pen, where nitrates were finally able to leach. On the other side, greater values of nitrates were found up to 3 m depth in Pen 2, which were directly related to rainy events. Resistivity may be regarded as a marker of soil salinity produced by manure and an indicator of variations of water content, organic matter and N–NO3− concentrations. The geophysical exploration by electrical resistivity tomography was successful in the design of soil sampling in a nonconventional application, such as the study of the distribution of nitrates in pens of animal feedlots.