Invasive alien aquatic plants (IAAPs) are increasingly transforming estuarine ecosystems under accelerating anthropogenic pressures. We mapped IAAP distribution across 290 South African estuaries using satellite imagery, citizen science, published records, and online databases, and quantified invasion susceptibility using National Biodiversity Assessment pressure ratings and Odds Ratio analysis. IAAP presence was assessed by biogeographical region and estuary type, with estuary type emerging as a stronger predictor. Results revealed that 69 systems (28%) support IAAPs, with Temporarily Closed Estuaries (TCEs) being most susceptible (40 systems). IAAP presence positively correlated with pollution (rho = 0.49; P < 0.001) and flow modification (rho = 0.35; P < 0.001). Highly polluted systems were 8.6 times more likely to be invaded, while flow modification increased invasion likelihood by 3.1 times. Two case studies investigated these dynamics. In the heavily urbanised Swartkops Estuary, flood events removed water hyacinth (
Pontederia crassipes
), yet mats re-established within three months and recovered to pre-flood coverage within six months. Assessment of five TCEs similarly indicated flooding as a mechanism for IAP flushing during open mouth periods, while IAP cover was highest during closed mouth periods characterised by oligohaline conditions. Controlled salinity experiments confirmed these field observations: plants thrived under freshwater (0), experienced rapid mortality under saline conditions (10), and showed transient growth before dieback under moderate salinity (5). These findings show that estuary connectivity, water quality, and hydrological regime interact to create or suppress IAAP invasion windows, with effective management requiring catchment-scale nutrient and flow regime interventions.