Fundamental differences between tropical and temperate Great Lakes are the continuously high temperature throughout the water column in tropical lakes and high rates of annual photosynthesis possible under continuously high solar irradiance. These aspects not only lead to permanent stratification and hypolimnetic anoxia in the deepest tropical lakes, but also they have consequences for oxygen concentrations throughout the water column and can dramatically affect the biogeochemical cycles of carbon, nitrogen and phosphorus. Denitrification and enhanced regeneration of phosphorus from metal oxides cause low nitrogen:phosphorus ratios in the deep waters of tropical lakes and create a nitrogen deficit when deep waters mix into surface waters which is met through N-fixation. Comparison of the whole lake nutrient budgets of Lake Superior and Lake Malawi demonstrate the effects of the preferential regeneration of phosphorus in Lake Malawi and loss of nitrogen. In the upper 200 m of permanently stratified Lake Malawi, nitrogen has a residence time of 2 years while in dimictic Lake Superior the nitrogen residence time is over 50 years. This disparity in the residence time indicates that nitrogen is poorly recycled to the mixed layer of Malawi. The physical climate of tropical great lakes affects nutrient biogeochemical cycles differently and imposes biogeochemical characteristics different from temperate lakes on the water quality. In particular, tropical lakes have low nitrogen to phosphorus ratios and chronic, anoxia which will lead to rapid proliferation of nitrogen fixing filamentous cyanobacteria when nutrient loading increases. The chronic hypoxia of tropical lakes will also enhance release of phosphorus bound to metal oxides and allow soil erosion to induce eutrophication in tropical lakes.