BackgroundPathogenic waterborne protozoa and helminths have the potential to cause infections in vulnerable populations such as children and immunocompromised individuals. Those residing in close proximity to wildlife‐protected areas in sub‐Saharan Africa, who are among the most economically disadvantaged, may have an increased susceptibility to these infections. This study aimed at detecting protozoan trophozoites/cysts, and helminth eggs in environmental and piped tap water (PTW) used by locals and tourists in the Queen Elizabeth Protected Area (QEPA) in western Uganda.MethodsWater samples were taken from the natural environment and domestic PTW sources. The samples were analysed for helminth eggs, free‐living amoeba (FLA) trophozoites/cysts, Cryptosporidium oocysts and Giardia cysts. The parasites were examined under the microscope, after which they were identified and counted. The data was subjected to univariate analysis to compare the prevalence rates across the different sample sites. The variables were summed using the mean and standard error of the mean.ResultsThe overall prevalence rates of the protozoan parasites, from highest to lowest, were as follows: 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 as follows: Strongyle (38.2%), Ascaris spp. (33.3%), Trematodes (25%), Strongyloides (10.5%), Toxocara spp. (8.3%) and Capillaria spp. (3.2%).ConclusionThe presence of parasites in natural water sources inside QEPA presents a significant hazard for the contamination of domestic water. It is imperative to implement established procedures for enhancing water quality.