This repository contains the modelling code and output data of an enzyme-based model for denitrification. One part of the code sets up the model to simulate a denitrification batch experiment based on ordinary differential equations. It solves the equations numerically and performs parameter estimation using the python package PyMC3. Details can be found in the related paper by Störiko et al (2021). The other portion of the code couples the reaction model to advective-dispersive transport and simulates denitrification at the river–groundwater interface in three scenarios with different hydrological conditions.