Reach scale experiments have shown that transient storage (TS) zones may be important controls on nitrogen (N) export to coastal waters. We investigated the relative impact that main channel (MC), surface TS (STS) and hyporheic TS (HTS) have on N removal at the network scale using an N removal model applied to the Ipswich River in Massachusetts, USA. Field investigations in 1^st through 5^th order reaches of the Ipswich River provided the scaling rules for hydraulic characteristics, indicating the size of STS and HTS relative to  MC (As:A) increases with stream size, whereas exchange coefficients are independent of size.  Nitrogen removal was simulated in the MC, STS and HTS compartments for every river grid cell using hydraulic characteristics, simulated discharge, and a constant removal rate (k) derived from LINX studies.  Model results indicate that on average, 55% of all runoff water molecules in the basin enter the HTS at least once, but enter the STS many times.  The MC dominates N removal in 1^st through 3^rd order streams, while in larger order reaches the STS and HTS predominate.  At network scales, all three have a roughly equal effect during baseflow periods.  These results help understand TS processes at basin scales.