Estuaries are well-known for their biodiversity and for the important ecological functions that they perform. The outflow of nutrient rich estuarine waters also enhances marine primary production and affects the structures the plankton assembles within the near-shore region. Estuaries are dynamic ecosystems with gradients in several physico-chemical factors (e.g. salinity, temperature, etc.) which in turn affect the biome present. Microbes, comprising mainly prokaryotes, are extremely abundant and diverse in aquatic ecosystems and as a consequence, play a major role in regulating key biogeochemical processes, including the carbon and nitrogen cycles. Microbial diversity studies in freshwater ecosystems, however, have received much less research focus despite their economic importance. Estuaries are unique in that they represent the convergence of marine and freshwater ecosystems. While a few studies have been done in estuarine microbial populations, most of the estuaries studies occur in the Northern hemisphere with very few analyses done in the Southern hemisphere. The aim of this study was to compare the microbial diversity present in the water column and sediment of the Kowie estuarine system as a function of 16S rRNA gene sequences.