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Riparian zones often act as nutrient filters, removing NO3 from water flowing through riparian soils. The role of vegetation in NO3 retention remains unclear and may be direct (uptake) or indirect (stimulation of microbial activity). We studied the riparian shrub Baccharis salicifolia (seepwillow) in Sycamore Creek (Arizona, USA), to determine (1) if sites colonized by seepwillow were sinks for NO3, and (2) the mechanism by which seepwillow causes NO3 retention. Subsurface water was sampled along flowpaths from an uncolonized gravel bar through seepwillow sites at several depths and on several gravel bars. NO3 concentration was significantly lower in seepwillow sites than in uncolonized sites, at least to 20 cm below the water table. Predictions of three hypotheses were tested to explain NO3 losses: (H1) by plant uptake, (H2) by stimulation of denitrification by seepwillow, and (H3) a prior condition unrelated to seepwillow. Six experiments were used to test these hypotheses, Transplant experiments, plant size relationships, and root distribution experiments all demonstrated the importance of seepwillow (rejection of H3). Other tests involving removal of aboveground biomass, denitrification measures, and mass balance calculations showed a predominance of denitrification over uptake (rejection of H1). We conclude that the main effect of seepwillow is to produce organic matter creating conditions favorable to denitrification and a loss of NO3 from subsurface water. Since denitrification is a permanent loss of N to the atmosphere, and uptake only temporarily retains N, the interaction between plants and microbes has important implications for the maintenance of water quality in streams and downstream reservoirs.