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Invasive species have become a major concern in the Danube. The Joint Danube Survey in 2007 found killer shrimps, Dikerogammarus villosus, at 93 % of the sites sampled along the river, Asian clams at 90 % and carpets of weeds at 69 %. Killer shrimps can adapt to a wide range of habitats and cause significant ecological disruption such as species reduction. The water hyacinth (Eichhornia crassipes) is considered one of the worst aquatic weeds in the world.

Over the past two centuries, the connection of the Rhine with other river catchments through an extensive network of inland waterways has allowed macro-invertebrate species from different bio-geographical regions to invade the river. A total of 45 such species have been recorded. Transport by shipping and dispersal by man-made waterways are the most important dispersal vectors.