The potential of enhancing water uses using soil aquifer treatment (SAT) is an interesting alternative for tropical regions, limited only by lack of knowledge on its performance in local conditions and the feasibility of adapting this technology. A SAT pilot study was conducted to analyze the phenomena associated with the transformation of organic matter (OM) from domestic wastewater. Chemically enhanced primary effluent collected at the Cañaveralejo wastewater treatment plant (Cali, Colombia) was used to feed pilot-scale SAT units at a rate of 1.25 m.d−1. Dissolved organic carbon (DOC) removal in a 5.0 m length and 0.1 m diameter column packed with sand was 64.4%, while a similar column packed with a Mollisol soil from Valle del Cauca region yielded 56.2%. Oxygen availability was an important factor in OM degradation, given that the sand column degraded OM aerobically and the soil column degraded OM under oxic as well as anoxic conditions. SAT acted as a reliable barrier for DOC in tropical conditions. Nevertheless, operational problems such as clogging indicated that probably Mollisol soil may not be the suitable for SAT or that this particular effluent requires further pre-treatment before SAT.