A 250 t sunflower oil spill in the Con Joubert Bird Sanctuary Wetland, South Africa, was the largest global sunflower oil spill in a freshwater wetland to date. Since there was insufficient historical data for the Con Joubert Bird Sanctuary Wetland prior to the spill, variations in phytoplankton assemblages were used to indicate wetland resilience in relationship with water quality variables. From this study, it was evident that the phytoplankton biodiversity was a more reliable indicator of wetland resilience than vegetable oil concentrations measured in the water column. Vegetable oil concentrations measured in the water column varied both spatially and temporally and can possibly be linked to the passive movement of drifting oil in the water column caused by wind action and temperature changes. While we were unable to pinpoint the exact mechanisms behind the increase in phytoplankton biodiversity, the response was probably driven by the degradation of the oil by natural microbial consortiums in the wetland or a possible increase in phytoplankton grazers. Certain phytoplankton genera were found to be tolerant to the adverse effects of the oil spill. These genera include Oedogonium, Cyclotella, Spirogyra,andPlanktothrix. In general, the univariate and multivariate statistical analysis showed a low diversity and richness at sites 1, 2 and 3 during the initial sampling surveys when compared to the remaining sites. However, the phytoplankton diversity and richness subsequently increased at all sampling sites from the second sampling survey, implying that there was a shift in phytoplankton biodiversity to a more stable state.