The US Environmental Protection Agency's Contaminant Candidate List includes Acanthamoeba spp. and Naegleria fowleri due to their ability to withstand harsh environmental conditions and their function as reservoirs for various important human pathogens. These human-pathogenic free-living amoebas (FLAs) pose significant challenges for their elimination from water systems because of their resistance to commonly used disinfectants, including those employed in treating drinking water. Our research group has previously isolated and detected cysts/amoebas of Acanthamoeba spp. in water from various open water systems across Bombali and Tonkolili Districts in Sierra Leone (SL), emphasising a potential public health risk to the Sierra Leonean population. We have used the emerging guidelines to decontaminate different environments, including open and drinking water systems, available in the UK Recovery Handbook for Biological Incidents (UKRHBI) to identify applicable recovery options (ROs) to mitigate the presence of FLAs in water systems in SL. The UKRHBI provides customised ROs for decontaminating/managing environments affected by any biological hazard, which are appropriately selected according to the physiological characteristics of the biological hazard (in this case, FLAs) and the characteristics of the site, following an accessible methodology. The following ROs might be applicable to the characteristics of the water systems and areas monitored: restricting water use, encouraging bottled water for drinking, removing contamination sources, modifying water treatment systems (e.g., integrating ozone-based treatments), and sludge treatment (use of ultrasonic disintegration treatment and topsoil stabilisation treatment). Emerging technologies, such as photolysis of sodium chloride and sodium hypochlorite, have demonstrated efficacy in inactivating Acanthamoeba castellanii and have the potential to be adapted to target other chlorine-resistant pathogens. The adoption of these interventions by the relevant authorities in SL could lead to the effective protection of vulnerable populations, including children, the elderly, immunocompromised individuals, and Ebola survivors.