Governments across the globe are currently besieged with the novel coronavirus (COVID-19) pandemic caused by SARS-CoV-2. Although some countries have been largely affected by this pandemic, others are only slightly affected. In this regard, every government is taking precautionary measures to mitigate the adverse effects of COVID-19. SARS-CoV-2 has been detected in wastewater raising an alarm for Africa due to the poor water, sanitation, and hygiene (WASH) facilities. Also, most countries in Africa do not have resilient policies governing sanitation and water management systems, which expose them to higher risk levels for the transmission of SARS-CoV-2. Therefore, this study unearthed the likely sources and routes of SARS-CoV-2 transmission in water systems (mainly wastewater) in Africa through a holistic review of published works. This provided the opportunity to propose sustainable remedial measures, which can be extrapolated to most developing countries in the world. The principal sources and routes of potential transmission of SARS-CoV-2 in water systems are hospital sewage, waste from isolation and quarantine centres, faecal-oral transmission, contaminated surface and groundwater sources, and contaminated sewage. The envisioned overwhelming impact of these sources on the transmission of SARS-CoV-2 through water systems in Africa suggests that governments need to put stringent and sustainable measures to curtail the scourge. Hence, it is proposed that governments in Africa must put measures like improved WASH facilities and public awareness campaigns, suburbanization of wastewater treatment facilities, utilizing low-cost point-of-use water treatment systems, legally backed policy interventions, and Community-Led Total Sanitation (CLTS). SARS-CoV-2 in water systems can be inactivated and destroyed by integrating ozonation, chlorination, UV irradiation, and sodium hypochlorite in low-cost point-of-use treatment systems. These proposed sustainable remedial measures can help policymakers in Africa to effectively monitor and manage the untoward impact of SARS-CoV-2 on water systems and consequently, on the health of the general public.