Lake Victoria is the world’s largest tropical lake and the third-largest water body, providingsignificant water resources for surrounding environments including the cultural, societal, andlivelihood needs of people in its basin and along the White Nile. The aim of this study was to usedecade-long time series of measured lake flow in the lake system and phosphorus deposition todevelop a suitable numerical model based on shallow water equations (SWE) for assessing waterquality in Lake Victoria, an increasingly important tool under climate variation. Different tech-niques were combined to identify a numerical model that included: i) a high-resolution SWEmodel to establish raindrop diffusion to trace pollutants; ii) a two-dimensional (2D) verticallyintegrated SWE model to establish lake surface flow and vertically transported wind speed flowacting on lake surface water by wind stress; and iii) a site-specific phosphorus deposition sub-model to calculate atmospheric deposition in the lake. A smooth (non-oscillatory) solution wasobtained by applying a high-resolution scheme for a raindrop diffusion model. Analysis with thevertically integrated SWE model generated depth averages for flow velocity and associatedchanges in water level profile in the lake system and showed unidirectional whole lake windblowing from the southwest to northeast. The atmospheric phosphorous deposition modelenabled water value assessment for mass balances with different magnitudes of both inflows andoutflows demonstrating annual total phosphorus at 13, 500 tons concentrating at mid-lakewestern and eastern parts. The model developed here is simple and suitable for use in assess-ing flow changes and lake level changes and can serve as a tool in studies of lake bathymetry andnutrient and pollution transport processes. Our study opens towards refining models of complexshallow-water systems