Ephemeral and intermittent streams are increasing with climate and land use changes, and alteration in stream water presence or flow duration will likely affect litter decomposition in channel and riparian zones more than dryland uplands. To investigate the influence of varying climate and stream flow regimes on rates of decomposition, we used a space-for-time substitution design and deployed common leaf litter over an 18-month period across a range of ephemeral to seasonally- intermittent stream reaches (10) and landscape positions (channel, riparian, upland) in Arizona, USA. The monitoring reaches were located in largely undisturbed military facilities, long term ecological research areas and a nature preserve. The most arid study washes, Black Gap (BG) and Sauceda Wash (SW), were located within the Barry M. Goldwater Air Force Base near Gila Bend, Arizona in the Lower Gila River Basin. Nine study sites were located on the Huachuca Mountains near Sierra Vista, Arizona and form part of the San Pedro River Basin. The study sites were located along 3 distinct elevations in 3 canyons: Huachuca Canyon and Garden Canyon which are located within the Fort Huachuca Army Post; and Ramsey Canyon, within the Nature Conservancy’s Ramsey Canyon Preserve (one was later dropped owing to a fire). We established three cross-sectional transects 100 m apart at each reach, except Sauceda and Black Gap Washes where there were 5 transects, and installed electrical resistance sensors (TidbiT v2 UTBI-001 data logger, Onset Corporation, Bourne, MA) at the thalweg of each cross-sectional transect to identify surface water presence frequency and duration. Consistent with expectations, rates of litter decomposition (k) decreased significantly in the channels as cumulative percentage (%) of water presence decreased below 40%. Indeed, differences in cumulative duration of water presence as well as channel bed material silt content explained 79% of the variation in k across flow regimes. Collectively, our findings suggest that rates of decomposition in intermittent stream channels will decrease with reduced duration of stream flow and water presence whereas rates in riparian zones will be less responsive to changes in climate and associated subsidies of stream flow.