The objective of this work was to analyse the distribution of the planktonic communities involved in the functioning of a 255-km river stretch and to get a better understanding of the influence of the river morphology on the diversity and dynamics of the micro-organisms. The planktonic communities (phytoplankton, bacterioplankton, proto-and metazooplankton) scarcely considered together in fluvial systems, were analysed at four sites of the Middle Loire during the low water period, in parallel to physical and chemical analyses. Physical and chemical variables such as turbidity, pH, suspended matter and chlorophyll a concentration were high, illustrating the classical, productive summer period. The algae played a major role in the water oxygenation until end-summer, then the algal drop concomitant to the bacterial sustained abundance appeared responsible for oxygen depletion. The downstream site enriched by nutrients inputs of two tributaries, carried the highest algal and bacterial densities. Situated in a meanders zone, the Middle Loire is characterised by a high habitat heterogeneity, the up-and downstream sites were wide and spread of vast standing zones and vegetated islands, whereas the two intermediate ones were narrower and more uniform. This morphological variability strongly impacted the micro-organisms diversity and distribution. Indeed, the algae and zooplankton composition were clearly influenced by the physical habitats of the river, the Cyanophyta were favoured by the lentic conditions and the Bacillariophyta by the turbulent ones, while the young stage of copepod and the large rotifer predators were indicator of a lentic origin. Thereafter, the river heterogeneity interfered with the zooplankton dynamics, the standing conditions enhancing the rotifer predation. In that way, we hypothesise that two opposite patterns characterised the wide sites spread of lentic water and the more uniform channels. In the first case, the zooplankton could prey on the ciliates protozoan, which in return favoured the flagellate ones; conversely in the second situation the zooplankton limited by the physical constraints did not impact the ciliates which could depress the flagellates. Thus, the similar geomorphology of the distant upstream and downstream sites (255-km apart) induced relatively close organisms distribution. Hence, disagreeing with the river continuum concept, this assertion shows the strong influence played by the local morphological characteristics of the Middle Loire in potamoplankton composition and dynamics.