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The main impacts from inland navigation on aquatic ecosystems are related to hydromorphological pressures such as the construction of groynes, the protection of river banks with rip-rap, deepening and maintenance of the channel (e.g. via dredging). Altering the shape of river courses to improve navigation affects the characteristics of river beds, river banks and the dynamics of sediment transportation. The effects can spread upstream and downstream over many years. Permanent changes to water levels and flows affect the whole river valley bottom and the ecology of floodplains. Navigation works tend to be designed to stabilise river channels in both space and time, which constrains the natural river dynamics of the river that are important for creating and renewing key habitats (ECMT, 2006). Thus, navigation requirements result in stabilized, ecologically uniform river channels, which lack natural in-stream structures and connectivity with the nearby floodplains (ICPDR, 2007).

Ship traffic also causes waves, which can disturb the reproduction habitats of fish and benthic invertebrates and impact aquatic plants. In addition, the engines of ships can cause an unnatural suspension of fine sediments, leading to reduced light for plant and algae growth (ICPDR, 2007). Further, navigable rivers are usually affected by numerous impoundments to achieve a uniform water level which, at the same time, disrupt river continuity and fish migration.

In addition to hydromorphological impacts, inland navigation can be a potential source of pollution coming from ship waste (oily and greasy ship waste, cargo waste, wastewater and household waste of passenger and hotel ships) or bilge water. There is also a risk of accidental spills, involving oil or hazardous substances, resulting from ship collision or damage (EC, 2018; ICPR, 2015). For example, on the river Rhine, in 2018 and the years before, oil released from shipping was the most frequently reported pollutant among suddenly occurring pollution incidents (ICPR, 2019).

Finally, to maintain navigable water levels in artificial canals that connect different river systems, water is often moved between rivers causing hydrological alterations but also the spreading of invasive alien species. Also, shipping is an important dispersal vector for invasive species between river systems, either by transport at the vessels or by release of bilge water.

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