This doctoral thesis aims to directly contribute to sustainable water resource management in Uganda by studying how differences in the physical attributes of its many crater lakes, specifically their shelter from wind, relative depth and frequency of deep water-column mixing affect their ecological vulnerability to water-quality loss when subjected to intensifying land use within their catchment. A quantitative understanding of these processes will allow local communities to decide which lake basins are most amenable to economic activity (crop agriculture, aquaculture, cattle watering), which lakes should be safeguarded as reservoirs of drinking water, and how much land use the latter category of lakes can tolerate without endangering this important function.