Nakivubo wetland, which has performed tertiary water treatment for Kampala city for the past 40 years, is ecologically stressed by agricultural and infrastructural developments. Field studies were carried out to assess the hydraulic loading, pollution profile, stability and water quality of this wetland. The upper and lower Nakivubo wetland receive 4.13−7.66 × 104 and 3.50−10.32 × 104m3/day of water respectively, of which 48.3–57.9% of total hydraulic loading to the upper wetland was carried by sampling station S1. The influent water to the upper wetland had a total BOD5 and NH4-N loading ranging from 2.6−4.4 × 103kg BOD/day and 0.79−1.68 × 103kg NH4-N/day respectively. The National Water and Sewerage Corporation's effluent constituted a large proportion of BOD and NH4-N loading into Nakivubo wetland. Zinc, copper and chromium were detected in trace amounts at most sampling stations. However, lead was occasionally detected at Kibira channel (station S5) at a concentration of 0.4mg/l, which is higher than the permitted Ugandan discharge limit of 0.1mg/l (NEMA 1999). The wetland showed a very high removal efficiency for BOD, ranging from 77.4%–86.3%, compared to ammonium-N which ranged from −66.1% to 33.1% indicating limitations with the nitrification process. A low self-purification for zinc, copper and chromium was also observed in the upper Nakivubo wetland, possibly due to poor plant-wastewater interaction resulting from wetland drainage. In the lower Nakivubo wetland conductivity and dissolved oxygen were generally higher in papyrus- than in Miscanthidium-vegetated zones. However, the BOD and ammonium-N loadings did not vary significantly (P = 0.217 and P = 0.359 respectively) between the two vegetated zones.