Abstract: Predicting N losses in flooded agricultural systems is complex because of the large number of potential N transformation pathways. Although coupled nitrification/denitrification at the flooded sediment near-surface oxic/anoxic interface is a recognized pathway of fertilizer N loss, the role of the newly discovered anaerobic ammonium oxidation (anammox) pathway in agricultural systems is poorly understood. A survey study was implemented to characterize sediment denitrification rates, anammox activity, and fluxes of ammonium and nitrate, and the vertical distribution of N functional genes were measured in Hawaiian taro (Colocasia esculenta) fields under three fertilizer management regimens (conventional, organic, and hybrid) as a model for flooded agroecosystems. Potential denitrification rates and anammox activity were measured using a slurry-based isotope pairing technique, and fluxes were determined by porewater modeling. Although significant numbers of anammox 16S rRNA genes were detected, only negligible anammox activity was found, illustrating the need to quantify not only the presence but also the activity of these bacteria. Quantitative polymerase chain reaction was performed for bacterial amoA, nirS, nosZ, and the 16S rRNA gene at 1-cm soil depth increments. Slurry isotope pairing technique–based potential denitrification rates (4.3–12.3 mmol N2 m−2 day−1) were on the high end of previous anaerobic incubation studies. Flux-derived denitrification rates were up to three orders of magnitude lower than slurry isotope pairing technique rates, suggesting strong nitrification regulation. Organically managed fields exhibited significantly lower slurry and flux-based denitrification rates than conventional and hybrid systems. This study supports the use of alternative fertilizer management techniques in flooded agroecosystems by the mitigation of N losses through denitrification and decreased overall N flux rates.