Micro-organisms, especially phytoplankton species, may be considered as potential indicators of local and more global changes in aquatic ecosystems and may thus constitute an excellent biomarker of water quality. Assessing biological, chemical and physical influence on phytoplankton regulation is a key process to understand population structure and dynamics, population diversity and succession, and to propose, if necessary and when possible, a human-hand control before any excessive algal proliferation could occur. Such issues are of main concern to help scientists and water managers to make possible for large-body reservoirs, lakes and ponds to reach the “good ecological state” recommended by the Water Framework Directive (WFD) by 2015. On first hand, our project aims to identify both the spatial and temporal phytoplankton structure and dynamics in the Reservoir Marne (located in the Seine catchment area), referred to as one of the largest reservoirs in occidental Europe. On a second hand, we try to understand the role of the various factors and processes (physical, chemical and biological) implied in both the distribution and the regulation of the phytoplankton. In 2006, i.e. the first year of the project, the reservoir has been sampled once a month in March and April and then, once every two weeks between May and September. To assess spatial heterogeneity, six stations and various depths for each station have been investigated. Water samples were obtained using a Van Dorn bottle for major nutrients, chlorophyll a, phytoplankton abundance and diversity, bacterial and viral abundance analyses. Zooplankton was sampled with a modified 30-L containing Schindler-Patalas box. Transparency was measured using a Secchi disk and light intensity with a LICOR probe. Oxygen concentration, pH and conductivity were determined using a multiparameter probe. Finally, a submersible fluorescence probe (FluoroprobeTM, bbe-Moldaenke) was used to discriminate and quantify the major algal classes in situ. We show that (i) the reservoir is not uniform as revealed by the phytoplankton abundance and structure which vary significantly from one sampling station to another, (ii) a clear seasonal dynamics can be observed for the different microbial communities with main differences on a vertical scale, (iii) in this context, a multitable analysis, still little used in aquatic ecology, is a powerful statistical tool to get a clear representation of the spatial and temporal organization of the assemblages of the different species.