Lake Victoria is the second largest freshwater lake in the world and the largest in Africa (Crul, 1995). According to Bugenyi & Magumba (1996), the ecosystem of Lake Victoria has undergone major changes during the past three decades, 1960s to 1990s. There have been declines in hypolimnetic oxygen (anoxia below 40 m seasonally), primary productivity of the lake appears to have risen to about 2 to 3 – fold, 35 - 55% of the bottom area of the lake now endures prolonged anoxia and the lake is now 0.5°C warmer than in the 1960s. Higher lake temperatures are associated with increased rainfall, with models predicting that some areas of lake Victoria basin region could receive 100 percent more rainfall when lake temperatures rise by as little as 1.5°C (Anyah & Semazzi, 2004). The study established the lake’s past environment and climate for the last about 12,000 years to present at selected sites of Lake Victoria on Ugandan side of the lake and the findings are timely to generate environmental history at sites which are prone to human activities on the Ugandan side of lake Victoria in order to inform policy makers and the pattern of past climate in the wake of the current global warming.