1. Introduction.- The origin of the lake.- The naming of the Madison lakes.- Ownership of Lake Mendota.- The regional setting.- 2. Physical Limnology.- Morphometry and Hydrography.- General Features of the Lake.- Hypsometry of Lake Mendota.- Climate of the Lake Mendota area.- Water budget of the lake.- Thermal structure and heat budget.- Water movement.- Summary. The four seasons in Lake Mendota.- 3. Chemistry and nutrient loading.- Chemistry of the lake water.- Nutrient loading studies.- Sediment composition and chemistry.- Recent sediments in Lake Mendota.- Oxygen in Lake Mendota.- Nitrogen in Lake Mendota.- Phosphorus in Lake Mendota.- Iron and manganese.- Sulfate.- Chloride.- Silica.- Inorganic carbon in Lake Mendota.- Summary.- 4. Phytoplankton.- Methodology for studying phytoplankton populations in Lake Mendota.- Annual cycles of phytoplankton.- Mean depth of chlorophyll.- Surface/volume ratios of phytoplankton cells.- Diatom blooms in Lake Mendota.- Blue-green algae of Lake Mendota.- Buoyancy of the blue-green algae of Lake Mendota.- Where do the algae go?.- Summary.- 5. Phytoplankton photosynthesis and primary production.- Methods.- Calculating whole lake productivity from incubator data.- Photosynthesis/light (P/I) relationship.- Photosynthetic efficiency of Lake Mendota phytoplankton 125.- Primary production in Lake Mendota.- A model for Lake Mendota production.- 6. Zooplankton.- Methods for studying Lake Mendota Zooplankton.- Species composition.- Zooplankton abundance.- Biomass of Zooplankton.- Conclusions.- 7. Bacteria, carbon cycling, and biogeochemical processes.- Methods.- Bacterial biomass and production in the water column.- The impact of Zooplankton feeding on bacteria.- Importance of bacterial attachment to particles.- A model for bacterioplankton growth and disappearance.- Significance of algal excretory products for epilimnetic bacteria.- Bacterial processes in the anaerobic deep-water sediments.- Sulfate reduction in Lake Mendota.- Conclusion.- 8. Higher Trophic Levels.- Bottom fauna.- Fish.- Summary.- 9. Long-term Change in Lake Mendota.- Chemistry and nutrient loading.- Oxygen in Lake Mendota.- Secchi transparency.- Phytoplankton.- Zooplankton.- Bacteria.- Fish.- Conclusion.- 10. Energy flow in the Lake Mendota ecosystem.- Appendix 1. Physical and chemical data.- Appendix 2. Phytoplankton data.