In a country like South Africa that is prone to drought, achieving good quality of water is necessary to ensure the nation's water resource sustainability in the interest of all water users (National Water Act (No. 36 of 1998). River flow and rainfall influence the estuarine environment and biological indicators (phytoplankton (chl a)), system variables (salinity, turbidity, dissolved oxygen, and temperature), and nutrients (phosphate, nitrate, and nitrite) are some of the core water quality variables considered in ecological reserve assessments. Globally, microplankton (phytoplankton and ciliate) community structure (composition, abundance, and biomass) varies with physico-chemical parameters, making them good bioindicators of water quality. Phytoplankton are one of the main primary producers in estuaries, forming the basis of trophic webs. Ciliates are a valuable tool for indicating hydrological conditions and trophic status and can be used as an additional bioindicator to phytoplankton. Characteristics that make ciliates potential bioindicators include very high metabolic rates, short generation times, broad geographic distribution, and their rapid response to changing environmental factors. Ciliates dominate the microzooplankton abundance in coastal water bodies and graze on phytoplankton directly, making ciliates ecologically crucial in transferring energy to higher trophic levels, and controllers of phytoplankton community structure, through top-down pressure on phytoplankton. The main attributes of ciliates used for water quality monitoring are feeding habits (bactivores, carnivores, omnivores, and algivores), species composition, abundance, and biomass.For each water quality variable, a concentration range (minimal ('excellent') to severely modified ('poor') within the water resource should be determined. This emphasises the importance of studying these variables in near-pristine water resources to determine the minimally modified concentrations. There are few microplankton community composition studies in South African oligotrophic or non-eutrophic systems that are important in determining reference conditions and community structures for possible future changes in 'Nazario' and his lovely wife Immaculata 'Ma Peng', Swiri 'Prof', Lum 'Maitre Spiritus', Njitse 'Njitse Made It' and Adamu 'Eidey' who always cheered me on. Lastly my love and thanks to my UKZN friends