One of humanity’s great challenges is to feed the growing world population. Fortunately, Canada is one of the Earth’s great “breadbaskets”. This country’s agriculture and agri-food system generates about 8% of the total Gross Domestic Product, and provides about one in eight jobs, a hugely important sector of the national economy. About 6% of the Canadian territory is farmed to grow crops and livestock, and much of the production is in proximity to water resources whose quality is important to both citizens and wildlife. Within this context, our team conducts research to evaluate and to devise means of managing the risk to water from contaminants generated in agricultural production. Our specific interests concern the ecology of enteric microorganisms in the agro-ecosystem; the fate of veterinary and human drugs following the application of manures or biosolids to soils; and the impact of agricultural production practices on the development of bacterial resistance to antibiotics. In partnership with numerous national and international collaborators, our experimental work is undertaken from the bench to the watershed scale. We utilize both conventional and molecular means to detect, enumerate, isolate and characterize indicator and pathogenic microorganisms obtained from environmental matrices impacted by agriculture. The sources of enteric pollution are elucidated at policy-relevant scales, and environmental bacteria are characterized with respect to human health risk. The microbial basis for the biodegradation in soils of pharmaceuticals, hormones and other organic chemicals of anthropogenic origin is investigated. Information from these studies is used to help inform the development of agricultural practices and policies that are protective of environmental quality and human health.