The environmental impact of reservoirs comes under ever-increasing scrutiny as the global demand for water and energy increases and the number and size of reservoirs increases.

Dams and reservoirs can be used to supply drinking water, generate hydroelectric power, increase the water supply for irrigation, provide recreational opportunities, and flood control. In 1960 the construction of Llyn Celyn and the flooding of Capel Celyn provoked political uproar which continues to this day. More recently, the construction of Three Gorges Dam and other similar projects throughout Asia, Africa and Latin America have generated considerable environmental and political debate. Currently, 48 percent of rivers and their hydro-ecological systems are affected by reservoirs and dams.

A dam acts as a barrier between the upstream and downstream movement of migratory river animals, such as salmon and trout.

Some communities have also begun the practice of transporting migratory fish upstream to spawn via a barge. The fish ladder is another method to transport migratory fish upstream.

Rivers carry sediment down their riverbeds, allowing for the formation of depositional features such as river deltas, alluvial fans, braided rivers, oxbow lakes, levees and coastal shores. The construction of a dam blocks the flow of sediment downstream, leading to downstream erosion of these sedimentary depositional environments, and increased sediment build-up in the reservoir. While the rate of sedimentation varies for each dam and each river, eventually all reservoirs develop a reduced water-storage capacity due to the exchange of "live storage" space for sediment. Diminished storage capacity results in decreased ability to produce hydroelectric power, reduced availability of water for irrigation, and if left unaddressed, may ultimately result in the expiration of the dam and river.

The trapping of sediment in reservoirs reduce sediment delivery downstream, which negatively impacts channel morphology, aquatic habitats and land elevation maintenance of deltas. Apart from dam removal, there are other strategies to mitigate reservoir sedimentation.

The flushing flow method involves partially or completely emptying the reservoir behind a dam to erode the sediment stored on the bottom and transport it downstream. Flushing flows aim to restore natural water and sediment fluxes in the river downstream of the dam, however the flushing flow method is less costly compared to removing dams or constructing bypass tunnels.

Flushing flows have been implemented in the Ebro river twice a year in autumn and spring since 2003, except for two dry years in 2004 and 2005. The construction of multiple dams on the Ebro river disrupted the delivery of sediments downstream and as a result, the Ebro delta faces a sediment deficit. The river channel also narrowed and bank erosion increased. During experiments, it was found that suspended sediment concentration during flushing flows is double that of natural floods, although the total water discharge is lower. This means that flushing flows have a relatively high sediment transport capacity, which in turn suggests that flushing flows positively impact downstream river ecosystems, maximising sediment delivery to the lowest reaches of the river. A total of 340,000 t/year of sediment could be delivered to the Ebro delta, which could result in a net accretion rate of 1 mm per year.