Spatial self-organisation of ecosystems is the process by which large-scale ordered spatial patterns emerge from disordered initial conditions through local feedbacks between organisms and their environment. Such process is considered important for ecosystem functioning, providing increased productivity, resistance and resilience against environmental change. Although spatial self-organisation has been found for an increasing number of ecosystems, it has never been shown so far for aquatic river vegetation. Here we explore the existence of spatial self-organisation of freshwater macrophyte patches in a typical lowland river (Belgium), showing that the underlying mechanisms for pattern formation are scale-dependent feedbacks between plant growth, water flow and local river bed erosion and sedimentation. The mapping of vegetation patches showed that the frequency distribution of patch sizes is governed by a power-law function, suggesting that the patches are self-organised. Scale-dependent feedbacks, likely to lead to this self-organised pattern, were demonstrated with a mimic experiment. Both positive and negative feedbacks on plants were confirmed by a transplantation experiment. Placing vegetation patch mimics in the river showed experimentally that on a short range (within and behind the mimics) flow reduction and increased sedimentation occurred, while on a larger range (next to patches) the flow was accelerated and decreased sedimentation took place. By transplanting macrophytes within, next to and further away from existing patches, it was proven that the conditions within the patches favoured the survival and growth of transplants (i.e. short-range positive feedback), while the conditions just next to patches led to decreased survival and growth (i.e. long-range negative feedback).