Anthropogenic nutrient enrichment is one of the key global change pressures threatening the health of estuaries. This is evident at the persistently eutrophic Swartkops Estuary located along the warm temperate coast of South Africa. Augmented nutrient-rich baseflows (e.g., stormwater runoff, wastewater treatment work discharges) have resulted in the persistent growth of invasive alien aquatic plants (IAAPs), particularly water hyacinth (Pontederia crassipes), in the upper estuarine reaches. As such, the objective of this study was to investigate the temporal population dynamics of water hyacinth in the Swartkops Estuary to inform management options. Methods included five-weekly sampling campaigns in winter, spring, and summer, interspersed with monthly sampling over a year-long period. Physico-chemical variables and river inflow were measured in situ, while samples were collected for inorganic nutrients, phytoplankton biomass, and IAAP measurements (cover, biomass, and tissue nutrients). Model results indicated that increased water temperature and inorganic nitrogen (ammonium and NOx) levels promoted increased coverage of water hyacinth, while seasonal analysis highlighted reduced (p < 0.05) dissolved oxygen levels during the peak summer IAAP accumulation period. Notably, model results indicated declining IAAP tissue TN and TP concentrations with increasing water temperature, yet overall TN and TP storage was highest in summer due to the extensive water hyacinth cover observed during this period. Overall, the proportionally low and transient nature of nutrient storage by water hyacinth populations, together with the detrimental consequences they facilitate, highlights the need to integrate short-term control measures with catchment-scale management interventions geared towards mitigating the causative drivers.