basalt and downstream – sedimentary), differ in their degrees of infill or depth. In each region, three cut-off meanders were examined; one in each region was impacted by gravel extraction (upstream deepening) and halieutic improvement (downstream deepening), whereas the others were left in their natural state having different silt accumulations either almost cut-off from the river or less silted-up and more open to the river. The sites were monitored for one year for physical and chemical characteristics. Diatom samples collected in summer 2009 were examined along with their associated biocenosis. The two catchments, differing in geology, land-use and water quality, sheltered different diatom communities. Physical and chemical differences were recorded between up- and downstream zones of each cut-off meander due to both the influence of the groundwater (buffering the water temperature among others) and the periodic inflow from the main channel (increased oxygen saturation concentration in downstream end of the cut-off meanders, except for the impacted upstream zone which contained a lot of macrophytes). In the upstream reach (except for one site), the connection with the groundwater from the surrounding catchment, which acts as a hydro-geological reservoir, might explain the highest mineralization and water hardness recorded mainly in the upstream zone of the cut-off meander, and the presence of Pseudostaurosira subsalina (Hustedt) Morales and Thalassiosira weissflogii (Grunow) Fryxell & Hasle. For the downstream reach, in addition to up- and downstream differences, other factors came into play giving rise to different communities, for example, cattle trampling in the cut-off meander leading to the presence of hypereutrophic and polysaprobic taxa or the potential local re-emergence of mineral springs associated with brackish taxa. Moreover, the up- or downstream deepening also induced differences: the extraction of sediment nearer to the river created a system in which water input from the main channel flows in through a larger opening, inducing allochthonous processes. This increased the river’s influence, creating a renewal of earlier morphological and ecological conditions, whereas the gravel extraction that modified the upstream zone increased the influence of groundwater from the surrounding catchment on this area of the site and led to water conditions independent of the main channel. Furthermore, this study has provided an important picture of the environmental variables, mechanisms and processes that drive the distribution of diatoms within the cut-off meanders along the Allier River, which can can be applied in future paleo-environmental studies.