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A subsurface flow wetland (SSFW) was simulated using a commercial computational fluid dynamic (CFD) code. The constructed media was simulated using porous media and the liquid resident time distribution (RTD) in the SSFW was obtained using the particle trajectory model. The effect of wetland configuration and operating conditions on the hydraulic performance of the SSFW were investigated. The results indicated that the hydraulic performance of the SSFW was predominantly affected by the wetland configuration. The hydraulic efficiency of the SSFW with an inlet at the middle edge of the upper media was 0.584 and the best among the SSFWs with an inlet at the top, the middle, and the bottom edge of the upper media. The constructed media affected the hydraulic performance by the ratio (K) of the upper and lower media resistance. The selection of appropriate media resistance in the protection layer can improve the hydraulic efficiency. When the viscous resistance coefficient of the media in the protection layer changed from 2.315×105 to 1.200×108, the hydraulic efficiency of the SSFW increased from 0.301 to 0.751. However, the effect of operating conditions on the hydraulic efficiency of the SSFW was slight.