The weir pools are the spaces formed by the raising of the water line and the slowing of the current caused by weirs, overflowing hydraulic structures, generally of small dimensions, very widespread in contemporary rivers. The nature of these environments is still poorly understood and water sciences struggle to classify them in known continental aquatic environments. Some see them as degraded segments of watercourses, which have totally or partially lost the typical features of lotic environments; others consider them as ecosystems as such, with their own functionalities and their own role to play in environmental dynamics. In a research that we have recently published, we equate weir pools operation with ecotones operation and we would like to explore this hypothesis in further detail in this paper. Indeed, weir pools and ecotones are controlled by environmental gradients and seem to have the same functionalities, such as the ability to filter matter, to store and redistribute substances and to provide a real habitat for different types of organisms. This new vision of weir pools can even be extended to other man-made aquatic environments, ponds for example. Thus, new research and management outlook arise as this type of environment will no longer be considered as a mere obstacle within rivers, but as environments which are fully integrated into today’s fluvial landscapes with their own functionalities.