The socio-economic well-being of South Africa is largely dependent on reservoir lakes. Contrastingly, the country lacks reservoir management skills and training, with a generation having passed since there was limited activity in this field. This review introduces two new, independent analyses which, using in-lake total phosphorus or satellite-measured chlorophyll-a, respectively, reveal that between 41% and 76% of total storage is eutrophic or hypertrophic. This is in stark contrast to a claimed 5% made by the responsible government agency (Department of Water and Sanitation). Data and information on the incidence and toxicity of cyanobacterial blooms are sparse, yet severe problems exist. There is a concentration of focus on water quantity, with absent parallel consideration of the additional limitations posed by poor water quality. The most seriously impacted reservoirs are located in the economic heartland of South Africa, which has an extant regional water quality crisis. The reasons behind the startling lack of attention to reservoir limnology, despite clear and long-standing warnings, are examined and placed in the perspective of an acknowledged and impending water crisis. It will take considerable time to up-skill South African limnologists to meet the needs highlighted by worsening reservoir water quality, and to offset the social and economic impacts that will transpire, if not timeously ameliorated. The responsible agency urgently needs to establish a reservoir-management programme that embraces remaining individual and institutional memory, integrates all available relevant knowledge and scientific findings, prioritises needs and acquires those skills and resources necessary to meet what is likely to become a crippling legacy of inaction.