Four different water sources (irrigation canals, small reservoirs, shallow wells, and tubewells), used for domestic purposes, in an irrigated area in southern Sri Lanka, were tested for Giardia spp. cysts and Cryptosporidium spp. oocysts. Identification of these parasites in water sources is important as these are increasingly recognized as causative agents of waterborne diarrhoeal disease. All the four sources of water were contaminated with cysts and oocysts. The sources of surface-water contained a greater number of protozoa compared to tubewells and shallow wells (p < 0.05). The results indicate a reduction of high parasite loads by natural filtration as the water moves from canals to shallow wells through the soil profile. This could present an opportunity to reduce the burden of diarrhoeal disease due to protozoa by selecting an appropriate source of drinking-water and identifying those water sources that require treatment solutions.