We examined seasonal and spatial linkages between N cycling and organic matter for a suburban stream in Maryland and addressed the question: How do longitudinal NH4+ uptake patterns vary seasonally and what is the effect of organic matter, stream size, transient storage and debris dams? We applied a longitudinal (stream channel corridor) approach in a forested stream section and conducted short-term nutrient addition experiments (adapted to account for the effect of nutrient saturation) covering 14–16 reaches, and compared two distinct seasons (late fall 2003 and late summer 2004). Longitudinal NH4+ uptake rate patterns had a distinct seasonal reversal; fall had the highest uptake rates in the upper reaches, while summer had the highest uptake rates in the lower reaches. This seasonal reversal was attributed to organic matter and evidenced by DON patterns. Transient storage did not have an expected effect on uptake rates in fall because it was confounded by leaf litter; litter produced higher uptakes, but also may have reduced transient storage. In summer however, uptake rates had a positive correlation with transient storage. Debris dams had no distinct effect on uptake in fall because of their recent formation. In summer however, the debris dam effect was significant; although the debris dams were hydraulically inactive then, the upstream reaches had 2–5 fold higher uptake rates. The seasonal and longitudinal differences in NH4+ uptake reflect interactions between flow conditions and the role of organic matter. Urbanization can alter both of these characteristics, hence affect stream N processing.