In some regions a significant long-term issue with reservoirs, irrespective of their use, can be the introduction or enhancement of exotic or native pest species.  The change in environment caused by storage creation can result in advantageous colonisation by species that are suited to the new conditions, and these may result in additional biological, social and/or economic impacts.  

Pest fauna species can have major impacts on waterways and their biota in the reservoirs and downstream, by directly preying on native species, or over-consuming the food and habitat supply for the natives.  In the downstream river systems major insect population blooms can occur, particularly for species naturally controlled by dessication, where the regulated river provides higher than natural year round flows.  

Pest flora species can occur within the reservoir, and in some instances proliferation may interfere with power generation (eg. clogging of intake structures) or downstream water use through changes in the quality of discharge water (eg algal bloom toxins, deoxygenated water).  Floating aquatic vegetation can have impacts on faunal species due to habitat degradation, and for public health by providing improved breeding grounds for mosquitos or other disease vectors.  Pest flora species in the downstream river system can successfully establish where modification of flooding regimes and loss of flushing flows provide suitable conditions.  Where schemes have diverted water out of a river system, weed species can invade areas of sediment accumulation and become solidly established.