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 1st through 5th order reaches of the Ipswich River provided the hydraulic and biogeochemical model parameters, indicating the size of the HTS relative to MC (As:A) was nearly twice the size of the STS, and the exchange coefficient of the HTS was about an order of magnitude lower than the exchange coefficient for the STS. 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, half of all runoff water molecules in the basin enter the HTS at least 2.65 times during its flow path through the river network, but enter the STS at least 32.3 times. The MC dominates N removal in all stream orders, but TS contributes nearly half of the total network N removal during summer low flow periods.