River structure and functioning are governed naturally by geography and climate but are vulnerable to natural and human-related disturbances, ranging from channel engineering to pollution and biological invasions. Biological communities in river ecosystems are able to respond to disturbances faster than those in most other aquatic systems. However, some extremely strong or lasting disturbances constrain the responses of river organisms and jeopardise their extraordinary resilience. Among these, the artificial alteration of river drainage structure and the intense use of water resources by humans may irreversibly influence these systems. The increased canalisation and damming of river courses interferes with sediment transport, alters biogeochemical cycles and leads to a decrease in biodiversity, both at local and global scales. Furthermore, water abstraction can especially affect the functioning of arid and semi-arid rivers. In particular, interception and assimilation of inorganic nutrients can be detrimental under hydrologically abnormal conditions. Among other effects, abstraction and increased nutrient loading might cause a shift from heterotrophy to autotrophy, through direct effects on primary producers and indirect effects through food webs, even in low-light river systems. The simultaneous desires to conserve and to provide ecosystem services present several challenges, both in research and management.