Biological invasions are a threat to protected areas globally; however, the relative lack of studies quantifying the ecological impacts impairs informed decision-making. We selected three annual alien plants, widespread in the riparian habitats of the Kruger National Park, South Africa: Datura innoxia, Parthenium hysterophorus, and Xanthium strumarium, to examine their potential impacts on riparian plant communities. We identified 12–13 populations for each and placed a pair of invaded and uninvaded plots in each population. Species richness, Shannon diversity, and Pielou evenness were compared between the invaded and uninvaded plots using LMM models, and species composition was compared using ordination. The invaded vegetation showed lower species richness compared to the uninvaded, with the strongest effect observed for P. hysterophorus. The invaded plots also showed lower Shannon diversity and Pielou evenness due to the presence of alien dominants. For all three invaders, the invasion resulted in changes in the composition of native vegetation. Some native plants were more frequent and abundant in the invaded vegetation, possibly due to the habitats created in sandy river beds. The native species richness decreased with increasing invader cover, but the species richness of aliens accompanying the invasive dominants was not negatively affected by their cover. Our results confirmed the negative impact of invasive aliens on native plant diversity, with the most pronounced effect by Parthenium hysterophorus invasions.