The historical trend of aggradation in stream beds of Europe's mountain and piedmont areas has been reversed since the beginning of the twentieth century to a general tendency towards narrowing and incision. After an overview of some causes and geomorphological effects of river bed incision, and a description of some case studies in alpine rivers, this paper aims to assess how the phenomenon affects the ecosystems of alluvial plains. The questions addressed are, in particular, the effect of river bed incision on sediment redistribution during floods, habitat diversity and the water table; and the consequences of these changes for the distribution and diversity of biological communities. The effect of incision on floodplain vegetation, instream invertebrate communities, groundwater and former channel ecosystems and fish communities are considered. It has been found that incision rarely affects the biocoenoses directly, but indirect changes in habitat conditions are significant. At the scale of the whole hydrosystem, the predicted impact of incision is a decrease in habitat heterogeneity, and, thereby, in biodiversity. At the ecosystem scale, the negative effect on biodiversity is higher in habitats that are less connected to the running water of the river.