Lake Geneva, located at the border between France and Switzerland, is the largest freshwater reserve in Western Europe. In the 70’s the economic importance of the lake made it necessary to develop a monitoring program that is still in action and provides data on physical and chemical characteristics as well on the abundance and species composition of planktonic communities. The analysis of the long-term data reveals important modifications of physico-chemical features of the lake, changes in the abundance, the structure, the phenology and the mechanisms of regulation of the planktonic and fish communities. In the last decades, the lake has undergone both a local anthropogenic pressure (increase and then decrease in phosphorus concentration) and a large scale atmospheric pressure that has induced synchrony in the long-term changes of water temperatures between lakes over the alpine area. These major forces have induced long-term trends in the different trophic levels. There is an increase in the abundance of one of the main planktivorous fish species, a decrease in the abundance of zooplankton and an increase in the biomass of phytoplankton. Such trends suggest a top-down control. However, a more acute analysis indicates complex mechanisms that combine both top-down and bottom-up controls varying in intensity depending on the time scale and population considered.