New Zealand's freshwater ecosystems are subject to microbial contamination from a predominantly agricultural landscape. This study examines the spatial and temporal distribution of the human pathogen Campylobacter in the lower Taieri River, South Island (New Zealand). Enumeration of thermophilic Campylobacter from river samples was performed using a most probable number (MPN) method. Seasonal variation in Campylobacter levels was evident, with higher median levels detected in summer, when human exposure through recreational water use is maximal. Campylobacter levels varied significantly among the 10 sampling sites, increasing below a major tributary entering the river and then showing a downstream decrease. These changes probably resulted from inputs from adjacent farms and instream Campylobacter losses (settling, death). Two main peaks in the flux of Campylobacter were observed, one in winter and one in summer. A decrease in notified cases of campylobacteriosis in the human population was observed when levels of Campylobacter at the main recreational bathing site on the river were low. Continuing land use change and intensification in New Zealand may lead to further increases in microbial contamination of freshwaters, and an associated increase in waterborne enteric diseases such as campylobacteriosis.