Wetlands often form an important component in the urban matrix, where they are largely disseminated. Despite the abundance of these urban waterbodies, little is known about the spread of alien aquatic plant species in cities. Ponds are frequent in urban parks and domestic gardens where terrestrial alien plant species are common. Therefore, urban ponds are likely to support many aquatic alien species which might disperse to the natural environment. To investigate this potential, we collected data from 178 ponds in a large European city (Geneva, Switzerland), across an urbanization gradient. 17% (23 taxa) of the aquatic flora appears to be nonnative, including five species at high risk of invasion. A large proportion of the waterbodies (43%) supported at least one alien taxa. Through the development of a risk assessment tool, the BGeneva-Aquatic Weed Risk Assessment system^, a risk map was created which revealed several alien species hotspots situated in the urban environment, but also in rural areas, including in protected wetlands. This risk mapping included the dispersal potential distance of species around these risk hotspots, and showed that most areas of dispersal seem to be relatively small. Ponds are target sites for deliberate introduction but they tend to be hydrologically isolated in the urban matrix, and these ‘islands’ therefore present a relative low risk of a wider dissemination of alien species. This risk is nevertheless expected to sharply increase in future. Introduction by humans is likely to be the main source of new alien aquatic plants, and so management should primarily aim to prevent the introduction of these species. Sites supporting alien species should also be monitored and, if possible, the species presenting a risk should be eradicated. Sites supporting alien species should also be monitored and, if possible, the species presenting a risk eradicated.