We conducted cross-sectional studies in the New York City Watershed to ensure a valid estimate of the risk associated with Cryptosporidium infection in dairy herds. Our aims were to obtain species-specific estimates of the prevalence of Cryptosporidium in dairy cattle and to investigate seasonal variations in prevalence. We validated our empirical estimates using a Bayesian approach. Samples were collected on 32 study farms, once in each of 3 different seasons using an age-stratified sampling design. The overall prevalence of Cryptosporidium parvum-like species and Cryptosporidium andersoni among the 1911 animals tested by the flotation method was 5% and 1%, respectively. Among preweaned calves (<65 days of age), the prevalence of C. parvum-like species was twice as high in the summer (26%) compared with the winter (11%). Herd prevalence showed the same seasonal trend. Preweaned calves were also shedding C. andersoni at an average intensity of 20 oocysts per gram of feces. We did not detect C. parvum-like oocysts in cattle older than 5 months. Sequencing of a portion of the 18s rRNA gene revealed that in the summer, 42% of the C. parvum-like oocysts shed by preweaned calves were zoonotic, compared with >74% during the rest of the year. Both empirical and stochastic methods revealed a summer peak in the prevalence of C. parvum-like oocysts in preweaned calves. Determining whether seasonal variation in the prevalence and proportion of Cryptosporidium species shed by preweaned calves is due to management practices or ecological factors will have important implications for effective control of this parasite.