Description: Denitrification, the microbial conversion of NO 3 - to N gases, is an important process contributing to whether lotic and riparian ecosystems act as sinks for excess NO 3 - from agricultural activities. Though agricultural waterways and riparian zones have been a focus of denitrification research for decades, almost none of this research has occurred in the irrigated agricultural settings of arid and semi-arid climates. In this study, we conducted a broad survey of denitrification potential in riparian soils and channel sediment from 79 waterway reaches in the irrigated agricultural landscape of California's Central Valley. With this approach, we sought to capture the wide range of variation that arose from diverse waterway management and fluctuating flow conditions, and use this variation to identify promising management interventions. We explored associations of denitrification potentials with surface water NO 3 - -N, organic matter, flow conditions, vegetation cover, near-channel riparian bank slope, and channel geomorphic features using generalized linear mixed models. We found strong associations of sediment denitrification potentials with reach flow conditions, which we hypothesize was the result of variation in microbial communities’ tolerance to dry-wet cycles. Denitrification potentials in riparian soils, in contrast, did not appear affected by flow conditions, but instead were associated with organic matter, vegetation cover, and bank slope in the riparian zone. These results suggest a strong need for further work on how denitrification responds to varying flow conditions and dry-wet cycles in non-perennial lotic ecosystems. Our findings also demonstrate that denitrifier communities respond to key features of waterway management, which can therefore be leveraged to control denitrification through a variety of management actions. This article is protected by copyright. All rights reserved.