The Hartbeespoort Dam is a discharge point of a catchment that is characterized by urbanization, mining, industrial, and agricultural activities. These activities coupled with fluxes of heavily polluted wastewater from informal settlements, wastewater treatment works, as well as runoff from golf courses have led to the development of recurring harmful algal blooms (HABs). The predominant cyanobacteria scum that is largely covering the Dam water is toxic to fish and poses serious public health risks. Phosphorus is the limiting nutrient in terrestrial aquatic systems and excess concentration in the waters usually results in eutrophication. The productivity level in Hartbeespoort Dam is also a function of total phosphorous (TP) level, showing a positive correlation with chlorophyll-a, an index for phytoplankton which are predominantly HABs in this Dam. Analysis of long-term in situ water quality data (1980–2020) show that TP is not the only driver, changes in surface water temperatures also affect the productivity level, especially, when TP levels are below a threshold of approximately 0.4 mg/L. Chlorophyll-a was retrieved from current generation high resolution satellite (Landsat and Sentinel) at 5-year interval. Standard band ratio-based ocean color model applied to satellite data produced an accuracy of R2 = 0.86 and RMSE of 5.56 µg/L. Time series analysis of in situ and satellite data show similar trends including capturing the effect of biocontrol on productivity levels between the late 1980s and the early 1990s, after which productivity increased with an increased flux of TP. Since 2015, the average annual surface temperature in the Dam has decreased leading to the decline in productivity level despite increasing levels of TP. The spatial dynamics of the HABs is a function of the discharges levels of the various rivers draining into the Dam as well as its geometry. Relatively higher concentrations are observed near river discharges and in areas of restricted water circulation.