This study investigates the effects of season, organic matter loadings, hydraulic conditions, recycling, and rapid drainage on water quality in a pilot-scale, three-stage subsurface flow constructed wetland (SSF CW) system. The pilot CW system consisted of a vertical flow-gravel filtration (v-GF) wetland in the first stage, a horizontal-subsurface flow (h-SSF) bed planted with Iris in the second stage, and a vertical-subsurface flow (v-SSF) bed vegetated with Phragmites in the third stage. The objective of this study was to evaluate the potential of these CW systems to remove organic matter from domestic wastewater on a pilot-scale three-stage SSF CW system. Comparisons of average influent and effluent concentrations showed that the multistage system could effectively reduce total suspended solids (TSS), biological oxygen demand (BOD) and chemical oxygen demand (COD) levels in effluent by as much as 98% and total organic carbon (TOC) by as much as 79%. Contributions of the first, second and third stages to the overall treatment were approximately 10%, 45% and 45%, respectively. The average TSS, COD, and TOC concentrations were reduced in the entire CW system by 70%, 80% and 90%, respectively. The BOD and TOC removal efficiencies displayed seasonal variations with average removals generally increasing in warmer seasons. Our results also demonstrate that there were strong correlations between removal efficiencies and loading rates. Average removals decreased with an increase in the hydraulic retention time (HRT). The rapid drainage and recycling operation increased the efficiency of BOD removal only.