Irregular waste disposal system, which results in the potential problem of groundwater and surface water contamination due to production of toxic leachate, has still now been considered as a very common practice in most of the developing countries including Uganda. Realizing the gravity of that problem, a study was conducted to develop a conceptual model considering all possible factors that usually take part in the hydrogeological processes of Lake Kiyanja watershed to assess the groundwater contamination vulnerability. Analysis of Groundwater boundaries, aquifer system, existing boreholes, recharge and discharge sources and the associated water balance were performed in developing the conceptual model. Using this, a numerical model was then developed with the help of Ground Water Modelling System (GMS). The specific solute transport model MT3DMS was used in simulation of this numerical model. The model shows that the contamination needs at least 27 years hours to reach near the outflux boundary. However, the contamination hazards from the landfill to the ground water will not be occurred immediately.