Waterborne protozoan parasitic diseases are considered a global disease. With no comprehensive review for the country, we evaluated only the available studies (n = 27) related to the waterborne transmission of protozoan parasites in Iran. The most commonly reported protozoan parasites were Acanthamoeba spp., Naegleria spp., Vahlkampfiid spp., Cryptosporidium spp., Giardia spp., Hartmannella spp., Saccamoeba spp., Entamoeba spp., Blastocystis spp., and other free-living amoeba. Immunofluorescence assay (IFA), polymerase chain reaction (PCR), loop-mediated isothermal amplification (LAMP), differential interference contrast (DIC), microscopic detection, and enumer-ation methods are the most reported methods to identify protozoan parasites in water samples. The literature showed untreated water, recreational water, and contaminated water supply sources by animal feces as the main routes of waterborne parasites transmission. No study reported stan-dard protocols to identify protozoan parasites. In addition, the investigation of protozoan parasites in water resource has not been performed all around the country. Iran, as a developing country, use surface water to supply drinking water. Many recreational rivers and springs can be potentially contaminated with parasitic protozoa and thus reliable surveillance systems need to be established. Furthermore, quick and applicable methods to survey the parasitic protozoa in water are necessary. © 2021 Desalination Publications.