Microbial contamination of surface waters is one of the most important water quality issues affecting the agricultural sector in Nova Scotia, Canada. Most farmers who irrigate in the province draw their source water directly from streams and rivers. One mode of pathogen transmission is the irrigation of horticultural crops with contaminated water. The extended storage of irrigation water prior to crop application could minimize this risk. Natural inactivation processes could, depending on the source water characteristics and length of storage time, reduce bacteria levels to acceptable use standards. The purpose of this project was to study bacterial population dynamics, specifically those of Escherichia coli, in shallow irrigation water reservoirs. Experiments, involving a series of dialysis tube survival studies, were conducted from May through September of 2006 in an operational farm reservoir to examine microbial inactivation kinetics. It was found that E. coli populations in the cool, lower layer (depth ≈ 3 m) did not decline, while populations in the warm upper layer (depth ≈ 1.0 m) experienced significant reductions over a period of several days. An inactivation model was calibrated and used to develop conservative estimates of T 90 , T 99 , and T 99.9 values for environmental conditions typical of the Annapolis Valley of Nova Scotia. If a shallow reservoir was well mixed to prevent gradients in temperature and dissolved oxygen, storage of irrigation water for a period of at least two weeks would reduce bacterial numbers by at least three logs during the growing season in Nova Scotia.