Topography plays a critical role in controlling rates of nitrogen (N) transformation and loss to streams through its effects on reaction and transport, yet few studies have coupled measurements of soil N cycling within a catchment to hydrologic N losses and sources of those losses. We examined the processes controlling temporal patterns of stream N export using hydrometric methods and dual isotopes of nitrate (NO3−) in a small headwater catchment on the coast of Northern California. Soil nitrate pools accumulated in the hollow during the dry summer due to sustained rates of net nitrification and elevated soil moisture, and then contributed to the first flush of NO3− in macropore soil-water and stream water in the winter. Macropore soil-waters had higher concentrations of all forms of N than matrix soil-waters, especially in the hollow. A plot of stream water δ15N versus δ18O values in NO3− indicated that NO3− was primarily derived from nitrification or microbial NO3−. Further analysis revealed a mixing of two microbial NO3− sources combined with seasonal progressive denitrification. Mass balance estimates suggested microbial NO3− was consumed by denitrification when conditions of high NO3−, dissolved organic matter, and soil-water contents converged. Our study is the first to show a mixing of two sources of microbial NO3− and seasonal progressive denitrification using dual isotopes. Our observations suggest that the physical conditions in the convergent hollow are important constraints on stream N chemistry, and that shifts in runoff mechanisms and flow paths control the source and mixing of NO3− from various watershed sources.