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 a human-hand control before any excessive algal proliferation could occur. Such issues are of main concern to help scientists and water managers to reach the “good ecological state” recommended by the Water Framework Directive by 2015. Part of our project aims to identify both the spatial and temporal phytoplankton structure and dynamics in the Reservoir Marne referred to as one of the largest reservoirs in occidental Europe. In 2006, the reservoir has been sampled once every two weeks between March and September. To assess spatial heterogeneity, six stations and various depths for each station have been investigated. 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 (iii) in this context, a multitable analysis is a powerful statistical tool to get a clear representation of the spatial and temporal organization of the assemblages of the different species.