Aquatic plants share a range of convergent reproductive strategies, such as the ability to reproduce both sexually and asexually through vegetative growth. In dryland river systems, floodplain inundation is infrequent and irregular, and wetlands consist of discrete and unstable habitat patches. In these systems, life history strategies such as long-distance dispersal, seed longevity, self-fertilisation, and reproduction from vegetative propagules are important strategies that allow plants to persist. Using two aquatic plants, Marsilea drummondii and Eleocharis acuta, we investigated the proportions of sexual and asexual reproduction and self-fertilisation by employing next-generation sequencing approaches, and we used this information to understand the population genetic structure of a large inland floodplain in western New South Wales (NSW), Australia. Asexual vegetative reproduction and self-fertilisation were more common in M. drummondii, but both species used sexual reproduction as the main mode of reproduction. This resulted in a highly differentiated genetic structure between wetlands and a similar genetic structure within wetlands. The similarity in genetic structure was influenced by the wetland in the two species, highlighting the influence of the floodplain landscape and hydrology on structuring population genetic structure. The high levels of genetic variation among wetlands and the low variation within wetlands suggests that dispersal and pollination occur within close proximity and that gene flow is restricted. This suggests a reliance on locally sourced (persistent) seed, rather than asexual (clonal) reproduction or recolonisation via dispersal, for the population maintenance of plants in dryland rivers. This highlights the importance of floodplain inundation to promote seed germination, establishment, and reproduction in dryland regions.