Linking two freshwater rivers is likely to to place the downstream channel in a state of disequilibrium, causing channel adjustments, erosion, sediment delivery to estuarine and marine systems. Some anadromous species have strict limits on their native waters, combining streams can alter their migration pattern, introduce species to areas not natural, alter habitats so no longer useful to some native species. But it is hard to predict or give exact effects.
Well it will be new experiment the results of which each of us speculating on the principles of ecology. natural succession also happened even this linkage develop naturally by changing courses of rivers. Though most of river linking projects are situated in same broad region which seldom has much difference in habitat change. Yes there will be certain ecological changes but not at larger scale of vanishing a particular species. ecosystem has dynamism to adjust the change.
Result of river linking is means mixing of different type of water which leads to disrupting aquatic life and changing ecology of the water will lead to death of marine diversity.
Transfer of water from one river to other ... i.e. surplus to deficit has positive effects on environment / ecology. It is essential to have water than no water situation for thriving ecology. Water enhances ecology /environment. Deficit river gets water when required which is essential for sustenance of aquatic life. There are large number of such water transfer cases in India operating for last several years....!
Linking of rivers means (inter-basin transfer of water), usually transferring of water from a river basin with surplus water to a river basin with deficient water. Hence there will be disturbance in the water regime in both the river basins and there will be definitely some impact on the living organisms (marine life-plant & animal) with the changed water eco-system. It may be negatively affect the eco-system in the river basin which looses water through transfer, but in all probability there will be positive impact on the eco-system in the river basin which receives water transferred from the adjacent river basin.
It depends on the river's water holding the impurities thereby the water quality is affected thus resulting in causing disturbance to the aquatic life when joins ocean. Also the dumping of the effluents and other polluted matters in the river is a major cause of harmful to aquatic system.