Nutrient uptake by phytoplankton in estuaries can mitigate the effects of anthropogenic nutrient loading and prevent excess nutrients from reaching adjacent coastal waters. In eutrophic estuaries, a shift typically occurs from a balanced benthic primary producer community (e.g., seagrasses, salt marsh) to a less stable, phytoplankton-dominated system potentially comprised of harmful algal bloom (HAB) taxa. Given this shift, this study investigated the role that phytoplankton play in influencing estuarine water column inorganic nutrient dynamics. To assess nutrient uptake capacity, dissolved inorganic nutrients (nitrogen (DIN), phosphorus (DIP), and silica (DSi)) and phytoplankton concentrations were assessed in relation to salinity. The mixing lines of DIN versus salinity plots were classified as “linear” (conservative, i.e., negligible uptake), “press” (concave curve, i.e., characteristic of the growth phase of the bloom), or “pulse” (complete depletion of nutrients, i.e., HAB events) as an indication of estuarine conditions. The majority (64%) of sampling dates exhibited press or pulse events indicating that the Swartkops Estuary presides in an undesirable state. Bloom species commonly consisted of the Heterosigma akashiwo (Raphidophyceae) and Cyclotella cf. atomus (Mediophyceae). Phytoplankton can take up to 98%, 18%, and 70% of the DIN, DIP, and DSi, respectively, but this comes with costs (e.g., hypoxia, food-web restructuring, increased turbidity) associated with HABs. Catchment-based nutrient reduction measures are thus critical to prevent degradation of ecosystem health and functionality in eutrophic estuaries.