This study aimed at comparing the performance of horizontal, vertical and hybrid subsurface flow system in polishing wastewater effluent from the maturation pond at Gusii wastewater treatment plant, Kenya. The treatments were monitored for six weeks duration for chemical oxygen demand, total suspended solids, total nitrogen and total phosphorous against Kenya’s National Environmental Management Authority standards for effluent discharge. Among the systems planted with Vetiver grass, the hybrid subsurface flow system significantly removed the pollutants more efficiently than the single operated systems. The Vetiver planted hybrid subsurface flow wetland systems achieved the highest removal of COD, TN, TP and TSS at 82.4, 87.9, 65 and 94.6%, respectively as compared to other wetland systems. The planted vertical subsurface flow removed COD, TN and TP at 72.9, 75.7, and 50.7%, respectively more efficiently than the horizontal subsurface flow system that achieved removal of COD, TN and TP at 65.3, 70.0 and 43.8%, respectively. The planted horizontal subsurface flow wetland however showed better TSS removal at 89.9% compared to 83.2% achieved by vertical subsurface flow system. The unplanted systems exhibited a similar trend whereby the hybrid subsurface flow systems achieved better performance than the single systems though with significantly (P≤0.05) lower organics and nutrients removal efficiencies compared to the planted systems.