Transportation of Cryptosporidium oocysts in river type source water is of great concern in an area where extensive human activities exist. In this study, a total of 47 samples were collected from Tongxiang, China, where drinking source water was taken from a complicated river network system, by three sampling campaigns over a rainy season in 2009, to reveal the presence, genotypes, and likely source of Cryptosporidium oocysts in river water. Immunofluorescence microscopy analyses show that 37 (78.7%) were Cryptosporidium positive, with a mean concentration of 0.51 oocysts per liter. These results suggest that the protozoa were commonly distributed in the river network type source water of Tongxiang with a relatively low concentration level. PCR analysis was used to determine the species/genotypes of Cryptosporidium, which revealed the presence of the animal related species/genotypes including Cryptosporidium suis, Cryptosporidium fragile, and the avian III, pig II, cervine genotypes. Three of them were also detected in wastewater samples taken from neighboring animal farms, showing that farm animals rather than human might be the major pollution sources. This is the first report on simultaneous detection and genotyping of Cryptosporidium oocysts from surface water in China.