A pilot-scale horizontal flow constructed wetland (HFCW) system planted with common reed (Phragmites sp.) was constructed to study how hydraulic loading rate (HLR), aspect ratio, water depth, and granular medium affect to the fate of several organic matter degradation intermediates namely, acetic acid (HAc), isovaleric acid (Isoval), and dimethylsulfide (DMS). ANOVA statistical analysis performed on the data set of 8 months of operation shows that the HLR and the water depth are two major factors that control the performance of HFCWs for the target analytes. A clear difference in the HFCW effluent concentrations was obtained according to water depth. Effluents of the shallow water depth contained lower DMS (1.05-1.44 microg l-1), HAc (7.91-10.9 mg l-1), and Isoval (0.11-0.15 mg l-1) concentrations than the deeper beds (DMS: 1.68-2.40 microg l-1; HAc: 9.29-14.4 mg l-1, and Isoval: 0.20-0.31 mg l-1). Such differences could be accounted to the different formation and consumption rates of the organic matter degradation intermediates, which is related with the redox potentials (E). Indeed, it could lead to different biochemical reactions of organic matter degradation according with the E value. HLR has a statistically significant influence on the effluent HAc, Isoval, and DMS concentrations. Seasonal variability of effluent HAc concentration shows that it is independent on the HAc loading. While the loading showed no seasonal pattern, the removal efficiency was clearly higher in cold months, which suggests a predominant internal production of HAc in HFCWs in the warm season from the accumulated organic particulate matter. Similar results were also found when Isoval and DMS were considered.