The aquifer storage and recovery system of Sant Joan Despí (SJD) in the Llobregat Basin (Barcelona, Spain) has been injecting potable water since its construction in 1969. In order to increase the environmental and economic sustainability of the process, the substitution of potable water by sand-filtered surface water (SFSW) has been considered. This study aims at assessing the clogging potential of SFSW by reproducing the aquifer storage and recovery (ASR) system in a column-type pilot system. Developed clogging of a metallic screen simulating a well screen in the ASR was observed by direct visualization and by scanning electron microscopy (SEM), and was measured by the pilot column head loss and by the analysis of extracellular polymeric substances formed. The results show that although there is a detectable clogging formation, the experiment could run with no flow limitation, suggesting that SFSW could be a feasible candidate water for aquifer injection in a real well demonstration phase.