In this study, the performance of a laboratory-scale soil aquifer treatment (SAT) system was investigated and treatability studies were done in order to determine organic matter removal from synthetic wastewater (SWW) and secondary treated real wastewater (RWW). The SAT system was constructed in laboratory conditions and treatability studies were conducted using soil columns, which were packed with silt loam soil samples. Each column was equipped with a series of ports at multiple depths from soil surface (10, 20, 30, 50, and 75 cm) to collect water samples. Two operational cycles were applied to represent the influence of different wetting and drying periods during wastewater application. Dissolved oxygen, chemical oxygen demand (COD), and total organic carbon (TOC) concentrations were measured in all samples. Average removal values of 61.4 % (COD) and 68.2 % (TOC) were achieved by in SWW and of 58.3 % (COD) and 51.1 % (TOC) in RWW in 55 and 25 weeks of operation, respectively. These results indicated that the performance of the columns operated with SWW was better than the performance of the columns operated with RWW. In essence, the easily biodegradable portion of organic matter was quickly consumed by microorganisms in the first 10 cm of the columns where oxygen levels peaked. Complex organic compounds that are likely to be found in RWW could thus be removed when longer residence times were achieved through the columns. When the removal performances achieved with different operating cycles were compared for each wastewater, it could be seen that longer wetting and longer drying periods yielded higher removal efficiencies in RWW and vice versa in SWW.