The objective of this study was to analyze atrazine (ATZ) spatial distribution in groundwater and present the factors related to its leaching potential in an area under intensive agricultural activity within the fluvio-Aeolian plain of the province of Córdoba, Argentina. Using tools such as soil and groundwater sampling and analysis, batch tests and numerical modeling, the variables that control the atrazine sorption and leaching potential were evaluated. The herbicide was detected in 14.7% of groundwater samples (0.14 to 1.26 μg L−1) becoming a leachable herbicide with moderate potential for groundwater pollution according to the calculated GUS (Groundwater Ubiquity Score) index. Hydrogeological characteristics influenced its distribution in the unconfined aquifer. Areas with a thin vadose zone (VZ) showed the highest atrazine levels, while the lithology of the vadose zone was also critical. In areas with a predominance of coarse-textured sediments (sands and gravels), low clay percentages and lower Koc, atrazine exhibits high mobility, which makes possible its transport to the unconfined aquifer at sites with a deep water table (≈25 m below surface). Herbicide spray application generally coincides with the rainy seasons, which contributes to high leaching rates. Numerical modeling indicated that transport of water and ATZ occurs both through micropores continuously, and macropores episodically. Groundwater has become a secondary environmental subsystem affected by the presence of ATZ due to advective, dispersive and reactive processes which allow its transport through the VZ. Even at relatively low concentrations, the presence of atrazine in groundwater requires long-term planning to monitor and control.