The population of the Ugandan capital city of Kampala has dramatically increased since the political turmoil of the 1970s and with it a considerable rise in industrialisation. Few manufacturing plants, however, have pretreatment installations in place for their polluted effluent prior to discharge into the surrounding ecosystems. Kampala’s main drainage system is the Nakivubo channel which empties directly into the neighbouring Lake Victoria, the second largest inland freshwater lake in the world. Increased urban effluent load coupled with reclamation for crop farming have considerably reduced the effectiveness of the wetland to filter out major pollutants, in particular heavy metals. Using atomic absorption spectrophotometry, this study showed that the efficiency in sieving out zinc (Zn), copper (Cu), cadmium (Cd) and lead (Pb) has shrunk from 89.7 – 98.3% in December 2006 to 79.4 – 92.1% in December 2008, over a period of three consecutive years. This is indicative of the growing ineffectiveness of the wetland to absorb heavy metals. Levels of the same metals in the lake water some two kilometres away from the mouth of the wetland have correspondingly increased from 23 - 31% to 35 - 47% in the same period. This poses a serious threat to the quality of the fish and to the over two million urban population that directly depend on the lake water for domestic and industrial use. The remedy lies in the relevant authorities to enforce pretreatment at each factory site, increased factory management sensitisation on environmental concerns and more stringent measures against wetland encroachment.