This paper demonstrates how mathematical modeling can contribute to improve understanding of lake behavior. Since the 60's Lake Bourget, one of the largest in France, had been suffering from eutrophication which was checked in 1980 by the diversion of the main sewers entering the lake. A research program was implemented between 1987 and 1990, including an on-site sampling campaign conducted concurrently with thermal and biogeochemical modeling of lake behavior. The model helped provide a better understanding of the ecosystem, displaying some processes hitherto misunderstood: (1) Winter overturn does not reach the bottom of the water column when the weather is mild. This leads to a incomplete reoxygenation of the hypolimnion and to redox conditions inducing the release of orthophosphate from the sediment, (2) Grazing by herbivorous zooplankton is getting more important in the control of spring algal growth as eutrophication of the lake regresses, (3) Settling of particulate phosphorus seems a complex and very important process in Lake Bourget, showing high sedimentation rates for particulate mineral phosphorus.