Denitrifying woodchip bioreactors (DWBs) have proven to be an efficient nature-based solution for nitrate removal. Modeling DWBs is required for improving their design and operation, but is hindered by the complexity of the modeled system where numerous chemical species and model parameters are needed. Reactions inside the woodchips are different from those at the edges, causing chemical localization (i.e., apparent simultaneous occurrence of incompatible reactions). We used the Multi Rate Mass Transfer (MRMT) approach to overcome these problems when simulating reactive transport processes in a DWB located at Kiruna, Sweden. Besides denitrification, other nitrogen-cycling processes (e.g., nitrification, dissimilatory nitrate reduction to ammonium, anammox) and alternative electron donors (e.g. oxygen, sulfate) were also considered. Biomass concentration is incorporated into the biochemical reaction rates, including growth and decay, to characterize microbial catalysis. We found that the MRMT model: 1) can account for the heterogeneity of the porous woodchips; 2) was capable of reproducing the nitrogen species evolution in the DWB with kinetic parameters from the literature; and 3) allows reproducing localized biochemical reactions (e.g., aerobic reactions on the woodchip edges, near the DWB entrance and anaerobic reactions inside); and 4) reproduces the full denitrification reactions sequence, but with the different reactions occurring in different portions of the woodchip (e.g., nitrate to nitrite near the edges and nitrite to nitrous oxide further inside). The latter observation suggests that increasing woodchip size may reduce the outflow of these undesired species.