Pathogenic water-borne protozoa and helminths sometimes cause debilitating infections in children and immunocompromised people, and the poorest of the poor communities living adjacent to wildlife protected areas in sub-Saharan Africa are at risk. This study aimed to assess the existence of protozoan cysts/ trophozoites, and helminth eggs in fresh surface and piped tap water utilised by locals and tourists in the Queen Elizabeth Protected Area (QEPA) in western Uganda. Water samples were taken from natural (environmental) sources and domestic water sources (piped tap water). The samples were analysed for helminth eggs, free-living amoeba (FLA) trophozoites, Cryptosporidium oocysts, and Giardia cysts. The parasites were examined under the microscope, after which they were identified, counted, and recorded. The overall prevalence of the protozoan parasites, from highest to lowest, were: FLA (56.6%), Cryptosporidium spp. (38.2%), Giardia spp. (36.5%), Eimeria spp. (20.3%), and Paramecium spp. (2.7%). Similarly, helminth parasite prevalence was: Strongyle (38.2%), Ascaris spp. (33.3%), Trematodes (25%), Strongyloides (10.5), Toxocara spp. (8.3%), and Capillaria spp. (3.2%). Necessary steps should be taken to improve the water quality in QEPA.