Aquifer storage and recovery (ASR) of freshwater in brackish or saline aquifers can be an efficient technique to bridge freshwater shortages in coastal areas. However, buoyancy effects may cause salinization at the bottom of the ASR well during recovery, making a part of the freshwater irrecoverable. This study shows how such freshwater losses can be reduced applying deep injection and shallow recovery by independently operated multiple partially penetrating wells (MPPW) in a single borehole. A small-scale ASR system with such an MPPW was installed in January 2012 and its operation was extensively monitored until October 2012. A SEAWAT model was built and calibrated on the field measurements of this first ASR cycle. The model was used to compare the MPPW with a conventional fully and partially penetrating well. The freshwater recovery of those wells was 15% and 30% of the injected water, respectively, which is significantly less than the 40% recovered by the MPPW. In subsequent cycles, no more than 60% could be recovered by the MPPW, as mixing in the lower half of the aquifer remained a source of freshwater losses. However, this recovery is significantly higher than the recovery of the conventional well types. This study therefore shows that for less ideal ASR conditions, a viable system can still be realized using MPPW. © 2013 Elsevier B.V.