To assess levels of faecal contamination in the Qu'Appelle River (Saskatchewan, Canada) and its suitability for irrigation, by using the Colilert-18/Quanti-Tray technology. Various sites located along the Qu'Appelle River were sampled weekly from May to August 2005-2007. A total of 594 freshwater samples were collected and analysed for enumeration of Escherichia coli using the Colilert-18. The false-positive rate for E. coli detection using Colilert-18 was at most 1.5%. Throughout the irrigation period (June to August), up to 85% of the water samples collected from one of the irrigation water-pumping sites exceeded the recommended limit of 100 CFU per 100 ml. Spikes in E. coli counts were generally concomitant with the sudden rise in river flows. A sub-sample of confirmed E. coli isolates were typed by randomly amplified polymorphic DNA (RAPD). RAPD analysis revealed a high degree of genetic diversity among E. coli isolates. A significant association between RAPD patterns and the month of E. coli isolation was demonstrated. Colilert-18 provides an effective means for assessing microbial quality of irrigation water. Qu'Appelle River is subject to variability of faecal contamination during irrigation times and monitoring throughout irrigation season is important for ensuring safe production practices.