Diatoms are a large and diverse group of algae which are distributed throughout the world in all types of aquatic systems and are one of the most important food resources in freshwater ecosystems. The need to sample diatoms arises from the necessity to know the history of the water quality. Diatom communities reflect the overall ecological integrity by integrating various stressors and as result provides a broad measure of their impacts. They are recognized as valuable organisms for bio assessment, due to their ease of identification, rapid life cycle and their visibility to the naked eye. Diatom communities provide interpretable indications of specific changes in the water quality Environmental gradients and assemblage composition in the Mnweni River catchment revealed that water chemistry, habitat structure, flow type and land use were the most important environmental factors for diatom assemblage composition in the Mnweni River. The results indicates that the diatom diversity and assemblage composition in the Mnweni River shows that changes in the water chemistry as well as organic pollution, but also indicate changes in the habitat character which is related to the water flow, river bank character and catchment land use. The diatom assemblages that were found at the sites are typical of clean or mildly enriched water conditions. The changing salinity in St. Lucia is the main physical factor that is driving the constant change in ecological conditions within the estuary. The changes in the diatom community structure in the estuarine system indicate the variable nature of the benthic communities under different salinity conditions. Contrary to the drought conditions that are being experienced, the diatom biomass did not show any significant changes or differences. This may be due to the rapid recovery ability that diatom communities exhibit in response to changes that are occurring in their environment. / Thesis (M.A.)-University of KwaZulu-Natal, 2006.