Invasive plant species are major drivers of biodiversity losses, particularly on islands that are vulnerable to invasions and extinction. The objective of this study was to document the vegetation structure and changes over time in two Nile Islands due to invasion by Vossia cuspidata (Hippo grass). One-hundred and one stands were assigned in three sites along the River Nile in Cairo, Egypt. Fifty-one associated species were recorded, belonging to 28 families. Annuals (Thereophytes) were the main life form in the area (51%) followed by helophytes (29%). Twelve vegetation groups were identified, representing the main communities in the studied stands. V. cuspidata was the dominant species and its maximum cover was recorded during the summer season. The lowest values for species diversity were recorded in open water, while the highest values were recorded in water edges and slopes of the riverbanks. There was up to 70% reduction in the cover of native species in the study area due to the invasion by V. cuspidata. Many native species were either disappeared or poorly recorded in the studied sites. Stem height and the cover of V. cuspidata in aquatic and riparian habitats lead to severe negative impacts on the growth and the diversity of native flora in the River Nile. Consequently, conservation of native flora through removing the invasive species should be a future priority along the River ecosystem.