The effect of preferential flow in soil pipes on nitrate retention in riparian zones is poorly understood. The characteristics of soil pipes and their influence on patterns of groundwater transport and nitrate dynamics were studied along four transects in a 1- to >3-m deep layer of peat and marl overlying an oxic sand aquifer in a riparian zone in southern Ontario, Canada. The peat-marl deposit, which consisted of several horizontal layers with large differences in bulk density, contained soil pipes that were generally 0.1 to 0.2 m in diameter and often extended vertically for 1 to >2 m. Springs that produced overland flow across the riparian area occurred at some sites where pipes extended to the peat surface. Concentrations of NO3−–N (20–30 mg L−1) and dissolved oxygen (DO) (4–6 mg L−1) observed in peat pipe systems and surface springs were similar to values in the underlying sand aquifer, indicating that preferential flow transported groundwater with limited nitrate depletion. Low NO3−–N concentrations of <5 mg L−1 and enriched δ15N values indicated that denitrification was restricted to small areas of the peat where pipes were absent. Groundwater DO concentrations declined rapidly to <2 mg L−1 in the peat matrix adjacent to pipes, whereas high NO3−–N concentrations of >15 mg L−1 extended over a larger zone. Low dissolved organic carbon values at these locations suggest that supplies of organic carbon were not sufficient to support high rates of denitrification, despite low DO conditions. These data indicate that it is important to develop a greater understanding of pipes in peat deposits, which function as sites where the transport of large fluxes of water with low biogeochemical reaction rates can limit the nitrate removal capacity of riparian zones. Copyright © 2011 John Wiley & Sons, Ltd.