The majority of South Africa’s fresh water (lotic and lentic), is eutrophic and this has resulted in water hyacinth, Eichhornia crassipes (C.Mart.) Solms. (Pontederiaceae) becoming South Africa’s most damaging aquatic macrophyte. Recently however, concerns have also been voiced over the presence of highly invasive submerged macrophyte species, such as Eurasian water-milfoil, Myriophyllum spicatum L. (Haloragaceae) in the Vaal River. Interaction studies between floating and submerged macrophytes have shown that floating macrophyte dominance restricts light penetration into the water column shading out submerged macrophytes while submerged macrophyte dominance reduces nutrient availability in the water column limiting floating macrophyte growth. This cycle ensures that these species cannot coexist in the same habitat for extended periods of time. The aims of this thesis were to: 1. Investigate changes in the historical and current macrophyte dominance in the Vaal River 2. Determine whether these changes could be attributed to stochastic events, such as floods and herbicide control measures. 3. The physio-chemical conditions of the water column, and whether pressure from herbivory by macroinvertebrates had possibly influenced Eurasian water-milfoil’s ability to dominate. Spatial and temporal analysis of satellite imagery revealed that water hyacinth and submerged macrophyte species dominated different regions of the study area over different periods of time from 2006 to 2010. This was significantly correlated with nitrate concentrations of the water column. One of the lower Vaal River Water Management Areas (WMA) had changed from a water hyacinth dominated state in 2006 to an alternative submerged macrophyte dominated stable state in 2008. It was concluded that this change could be attributed to: a stochastic flooding event in 2006; perturbation from integrated control measures implemented against water hyacinth; and low nitrate concentrations of the WMA. The lack of any substantial macroinvertebrate herbivory pressure or control measures implemented against Eurasian water-milfoil, compared to similar surveys conducted in the U.S.A. and its native range in Eurasia was shown to contribute to its dominance. Future successful integrated control programmes, including biological control against Eurasian water-milfoil, could provide the perturbation required to restore the ecosystem. However, without the reduction in nitrate concentration levels, water hyacinth will remain the dominant stable state of the rest of the Vaal River.