Technical Abstract: Oysters were collected 8 times from 7 sites in the Chesapeake Bay or its tributaries with accompanying data on water temperature, salinity, rainfall, and streamflow. Gill washings were examined by immunofluorescence microscopy for Cryptosporidium oocysts. Of 1590 oysters, 19.6% had detectable oocysts. Of 53 collections, oocysts were detected 81% of the time. The time when the greatest percentage of oysters at most sites had detectable oocysts coincided with the time of greatest weekly and monthly rainfall, greatest stream flow into the Bay, and lowest water temperatures. Cryptosporidium parvum genotype 1 and 2, and C. baileyi were identified by PCR and gene sequencing. Oocyst infectivity was confirmed from 37.5% of the collections by initiating infections in mice. These data indicate a significant relationship between high rainfall, high streamflow, low water temperature, and the presence of Cryptosporidium in oysters. The impact of rainfall on dissemination of animal feces into surface water is an important factor related to manure management in animal agriculture.