Lake Bourget, located in the Alps region, is the largest natural French lake. It constitutes an important reservoir of drinking water for thousands of inhabitants. In the 60's, the first occurrence of eutrophication has been observed in Lake Bourget. In order to tackle the eutrophication, many restoration programs have been implemented since the 1970s. The massive reduction in nutrient loads (phosphorus and nitrate) has improved the water quality over the past two decades. In 2008, according to OECD trophic categories, Lake Bourget is classified as mesotrophic. However, blooms of the filamentous, phycoerythrin-rich, non-nitrogen fixing and hepatoxic cyanobacterium Planktothrix rubescens have occurred since 1996. The first objective of this work is to use the one dimensional vertical (1DV) thermal and biogeochemical model to simulate the lake temperature during 3 decades (1976-2008) in order to study the pluriannual water temperature evolution. The second objective involves studying the phytoplankton dynamics, in particular Planktothrix rubescens which dominates Lake Bourget phytoplankton for the last tens years despite the restoration efforts. This study on phytoplankton dynamics is focussed on two years 2003 and 2008 where environmental conditions are representative of the variability of Planktothrix rubescens' development.