Intensification of dairying on irrigated pastures has led to concern over the microbial quality of shallow groundwater used for drinking purposes. The effects of intensive dairying and border-strip irrigation on the leaching of E. coli and Campylobacter to shallow groundwater were assessed over a three-year period in the Waikakahi catchment, Canterbury, New Zealand. Well selection excluded other sources of contamination so that the effect of dairying with border-strip irrigation could be assessed. Groundwater samples (135) were collected, mostly during the irrigation season, with E. coli being detected in 75% of samples. Campylobacter was identified in 16 samples (12%). A risk assessment of drinking water with these levels of Campylobacter was undertaken. A probability distribution was fitted to the observed Campylobacter data and the @RISK modeling software was used, assuming a dose response relationship for Campylobacter and consumption of 1 L/day of water. The probability of infection on any given day in the study area was estimated at 0.50% to 0.76%, giving an estimated probability of infection during the irrigation season of 60% to 75%. An epidemiological assessment of the Canterbury region comparing areas encompassing dairy within major irrigation schemes (∼55% border-strip irrigation) to two control groups was undertaken. Control group 1 (CG1) encompasses areas of dairying without major irrigation schemes, and a second larger control group (CG2) comprises the rest of the Canterbury region. Comparisons of the subject group to control groups indicated that there was a statistically significant increase in age-standardised rates of campylobacteriosis (CG1 Relative Risk (RR)=1.51 (95% CI = 1.31-1.75); CG2 RR = 1.51 (1.33–1.72)); cryptosporidiosis (CG1 RR = 2.08 (1.55–2.79); CG2 RR = 5.33 (4.12–6.90)); and salmonellosis (CG2 RR = 2.05 (1.55–2.71)).