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The water quality in the Inner Murchison Bay (IMB) located in Uganda on the northern shores of Lake Victoria is affected by a complex mixture of processes and driving factors including pollution, river inflows, lake water levels, wetland management and flora and fauna populations. This study attempts to explain long-term variations of the IMB water quality and to provide a plausible water quality model. Because intermittent monitoring around the Bay hinders accurate determination of pollution, concentrations at the extreme northern shores (hotspots) are considered indicative of the pollutant loading into the bay. Delft3D-Flow was applied to study the Bay hydrodynamics and coupled with the Delwaq module to investigate water quality processes related to oxygen: organic and nutrient components i.e. dissolved oxygen (DO), biological oxygen demand (BOD) and ammonium (NH 4 + ). It is found that the IMB water quality deteriorated exponentially in the period 2001-2014 due to increased pollution and the high residence time of water. The worst water quality was in 2010 when diffuse pollution intensified due to the lining of more drainage channels within Kampala City in addition to the declining wetland effect. The water quality towards the Outer Murchison Bay (OMB) deteriorated over time with dilution accounting for 40-60% of pollutant reduction. Although the effect of lake level variations is negligible compared to pollution into the IMB, increased lake levels after 2011 improved DO levels and mixing and hence BOD levels in the IMB.