1. The Vaal River is a vital water source for domestic, industrial, and agricultural use in South Africa’s economic heartland. However, its water quality is under increasing pressure from nutrient pollution, algal blooms, and invasive aquatic plants. This study applies the Algal Problem Index (API) to assess biological water quality and identify potential risks associated with cyanobacteria and algae in the upper reaches of the Vaal River. 2. Water samples were collected over a 12-month hydrological year from 16 sites, including two impoundments and four major tributaries. Physicochemical parameters were analysed alongside chlorophyll- a concentrations, phytoplankton identification, and multivariate statistical techniques to evaluate relationships between environmental parameters and algal-related problems. 3. Results revealed that several taxa, including Microcystis aeruginosa and Dolichospermum circinale, are responsible for taste, odour, and potential toxin production. Tributaries such as the Riet Spruit and Klip River were identified as major sources of nutrient loading and organic pollution, although low light penetration in the Klip River limited algal proliferation. Elevated API scores, indicative of degraded biological water quality, were recorded downstream of nutrient-rich tributaries where light availability facilitated algal growth. Canonical correspondence analysis showed that problematic algal taxa correlated strongly with elevated temperatures, turbidity, and nutrient concentrations, particularly during summer. 4. The API proved to be a valuable monitoring and communication tool to provide a visual and practical assessment of water quality risks. These findings highlight the importance of continued monitoring and integrated catchment management to mitigate ecological and public health risks in the Vaal River system.