Outbreaks of cryptosporidiosis have been linked to weather patterns such as heavy precipitation. However, outbreaks only account for a small percentage of all cryptosporidiosis cases and so the causes of the majority of cases are uncertain. This study assessed the role of environmental factors in all cases of cryptosporidiosis by using ordinary least-squares regression to examine the relationship between the monthly cryptosporidiosis rate, and the weather and river flows in England and Wales between 1989 and 1996. Between April and July the cryptosporidiosis rate was positively related to maximum river flow in the current month. Between August and November cryptosporidiosis was also positively linked to maximum river flows in the current month but only after accounting for the previous month's temperature, precipitation and monthly cryptosporidiosis rate. No associations were found between December and March. Through an understanding of the environmental processes at work, these relationships are all consistent with an animal to human transmission pathway especially as the relationships vary throughout the year. This study therefore indicates the importance of an animal to human transmission pathway for all cases of cryptosporidiosis.