Building dams and channels reduces downstream river flows and changes the hydrology of entire river systems with impacts on all life in the watersheds. Over-extraction of water for agriculture can alter water habitats and limnic fauna from biodiverse communities to poor systems with only few species. Note that about half of the amphibian species in Europe are threatened.
Water tables may be altered as groundwater recharge in the area is increased on the irrigated areas, but may be reduced where the water is taken. With changing hydrology, ecologically important wetlands or flood forests dry out, change the character or disappear completely. Such wetlands are core-habitats in arid and semi-arid landscapes, providing drinking water for many species, taking important roles e.g. for bird migration, and having numerous other ecological functions. Rain fed cereal areas in semi-arid areas are habitats for a diverse community of fauna and flora, including endangered steppe birds and rare plant species with very high environmental value. Here, irrigation can cause another problem for biodiversity: irrigated crops often grow more dense, quicker and higher. This has consequences for many species, e.g. in terms of breeding sites, movement inside the crops, bare grounds for foraging etc.