Reach scale experiments have shown that transient storage (TS) zones may be important controls on dissolved inorganic nitrogen (DIN) export to coastal waters. Here, we investigated the relative impact that main channel (MC), surface TS (STS) and hyporheic TS (HTS) have on DIN removal at the network scale using a DIN removal model applied to the Ipswich River in Massachusetts, USA. Collaborative field investigations in 1st through 5th order reaches of the Ipswich River provided the mean and range for each hydraulic parameter, indicating the size of HTS is nearly twice that of STS and the exchange coefficient (α) between MC and STS is about an order of magnitude greater than between MC and HTS. DIN removal was simulated in the MC, STS and HTS compartments for every river grid cell using hydraulic characteristics, simulated discharge, and a constant reaction rate (kt) derived from LINX2 studies. Model results indicate that although MC-STS connectivity is significantly greater than MC-HTS connectivity at the reach scale, there is a high probability of water entering the HTS at some point along its flow path through the river network. Results indicate the MC, STS, and HTS all have the potential to strongly influence network scale DIN removal and highlights the importance of partitioning between non-advective zone processes.