The Vaal Dam catchment, which is the source of potable water for Gauteng province, is characterized by diverse human activities, and the dam encounters significant nutrient input from multiple sources within its catchment. As a result, there has been a rise in Harmful Algal Blooms (HABs) within the reservoir of the dam. In this study, we employed time series analysis on nutrient data to explore the relationship between HABs, using chlorophyll-a (Chl−a) as a proxy, and nutrient levels. Additionally, Chl−a data extracted from Landsat-8 satellite images was utilized to visualize the spatial distribution of HABs in the reservoir. Our findings revealed that HAB productivity in the Vaal Dam is influenced by the levels of total phosphorus (TP) and organic nitrogen (KJEL_N), which exhibited a positive correlation with chlorophyll-a (Chl−a) concentration. Long-term analysis of Chl−a in-situ data (1986–2022) collected at a specific point within the reservoir showed an average concentration of 11.25 μg/L. However, on certain stochastic dates, Chl−a concentration spiked to very high values, reaching a maximum of 452.8 μg/L, coinciding with elevated records of TP and KJEL_N concentrations on those dates, indicating their effect on productivity levels. The decadal time series and trend analysis demonstrated an increasing trend in Chl−a productivity over the studied period, rising from 4.75 μg/L in the first decade (1990–2000) to 10.51 μg/L in the second decade (2000–2010), and reaching 16.7 μg/L in the last decade (2010–2020). The rising averages of the decadal values were associated with increasing decadal averages of its driving factors, TP from 0.1043 to 0.1096 to 0.1119 mg/L for the three decades, respectively, and KJEL_N from 0.80 mg/L in the first decade to 1.14 mg/L in the last decade. Satellite data analysis during the last decade revealed that the spatial dynamics of HABs are influenced by the dam’s geometry and the levels of discharge from its two feeding rivers, with higher concentrations observed in meandering areas of the reservoir and within zones of restricted water circulation.