Although the presence of protozoa in drinking water is a major public health problem in many countries, knowledge about the risks of these organisms in the anthropogenic environment in Paraguay is still scarce. Giardia spp. and Cryptosporidium spp. are pathogenic protozoa with faecal-oral hydric transmission that cause gastrointestinal disorders which reflexes may be severe for children, old-aged individuals and immunocompromised people. The research aims to investigate oocysts of Cryptosporidium spp. and cysts of Giardia spp. in water samples from four rivers that cross the city of Asunción, capital of Paraguay. Water samples were collected from the Riachuelo, Antequera, Peru and Mburicaó rivers. The spontaneous sedimentation technique was used for all water samples to concentrate the particulate material. For the research of cysts of Giardia spp. slide-coverslip preparation was used. For the search for Cryptosporidium spp. Ziehl-Neelsen staining was used. The results presented positivity for both oocysts of Cryptosporidium spp. and cysts of Giardia spp. in the water samples that were collected in the Antequera, Peru, and Mburicaó rivers, and only Cryptosporidium spp. in the waters of the Riachuelo River. The concentration of cysts and oocysts per microscopy field was higher in the Mburicaó river sample and, in decreasing order, in Peru and Antequera rivers. The concentration of Cryptosporidium spp. in the sample of the Riachuelo River was lower than the other samples. This was the first record of Cryptosporidium spp. in rivers of Paraguay in the scientific literature. We concluded that waters of urban rivers of the city of Asunción are contaminated with oocysts of Cryptosporidium spp. and cysts of Giardia spp. through the domestic sewage discharge. It is recommended that the population be advised to avoid contact with water from contaminated rivers and that sanitation measures to improve river water quality should be adopted by health authorities.