Artificial recharge of aquifers is a technique for improving water quality and increasing groundwater resources. Understanding the fate of a potential contaminant requires knowledge of the residence time distribution (RTD) of the recharged water in the aquifer beneath. A simple way to obtain the RTDs is to perform a tracer test. We performed a pulse injection tracer test in an artificial recharge system through an infiltration basin to obtain the breakthrough curves, which directly yield the RTDs. The RTDs turned out to be very broad and we used a numerical model to interpret them, to characterize heterogeneity, and to extend the model to other flow conditions. The model comprised nine layers at the site scaled to emulate the layering of aquifer deposits. Two types of hypotheses were considered: homogeneous (all flow and transport parameters identical for every layer) and heterogeneous (diverse parameters for each layer). The parameters were calibrated against the head and concentration data in both model types, which were validated quite satisfactorily against 1,1,2-Trichloroethane and electrical conductivity data collected over a long period of time with highly varying flow conditions. We found that the broad RTDs can be attributed to the complex flow structure generated under the basin due to three-dimensionality and time fluctuations (the homogeneous model produced broad RTDs) and the heterogeneity of the media (the heterogeneous model yielded much better fits).We conclude that heterogeneity must be acknowledged to properly assess mixing and broad RTDs, which are required to explain the water quality improvement of artificial recharge basins.