A study was carried out within a 700-km river sector, including three types of ecosystems (a reservoir, a river and its estuary) to characterise the major features of zooplankton communities in the Seine Basin. In rivers, zooplankton biomass becomes significant only when the growth rate of the organisms is higher than the dilution rate (4-5th orders rivers, according to River Continuum Concept). Upstream, short residence times favour the development of small species (Rotifers) with low individual body weight and biomass. Conversely, larger species (microcrustaceans) develop more downstream, where increased residence time leads to autochthonous production (Riverine Productivity Model). Such a pattern is greatly modified by human impact. Zooplankton input from the Marne reservoir represents one type of disruption in the general upstream-downstream trend (according to the Serial Discontinuity Concept). This reservoir is a source of microcrustaceans; they rapidly disappear mainly through fish predation, and therefore have little impact on the river phytoplankton. Discontinuities, such as confluences, have a relatively small effect on the stock of zooplankton with regard to the water release from the reservoir, but they persist more downstream, because they have the same lotic origin. A few microhabitats with macrophytes play a small role for this canalised river, but they can modify locally the plankton community structure and composition. As a whole, the flux of zooplankton rises exponentially, whereas discharge increases linearly from upstream (4th order) to downstream (8th order). In the canalised sectors, Dreissena larvae build up an important biomass, adding to that of the zooplankton sensu stricto. Especially abundant in the downstream sector of the Marne and Seine Rivers, the larvae show a widespread colonisation of the benthic substrates by the adult Dreissena. One of the largest mussel colonies in the middle estuary can contribute to a rapid decrease of zooplankton. Estuary ecosystems form a transitional zone between freshwater and seawater, with zooplankton dynamics closely linked to the particular conditions on this part of the river system.