The provided files accompanies the manuscript "A comprehensive porewater isotope model for simulating benthic nitrogen cycling: Description, application to lake sediments, and uncertainty analysis". All files are provided within zip folders to maximize file transfer. The folders include: Scripts.zip Julia codes needed to run the model (also accessible at https://gitlab.com/p.reichert/Nsediment/-/tree/master/Scripts?ref_type=heads) R scripts ProcessInferenceResults.R -> to process model outputs obtained upon Bayesian inference ProcessPredictionResults.R -> to process model outputs obtained upon prediction (to assess output uncertainty) ProcessSimulationResults.R -> to calculate the depth-integrated rates for the different reactions Data zip folder: Porewater data from the sampling campaign on Lake Lucerne in April 2021, used for the assessment and validation of the model. Concentrations of: O2, NO3, NO2, NH4, SO4. N isotopic composition of NO3 and NH4. Scenarios zip folders: With all model outputs, including results of inference and uncertainty prediction Scenarios considered for the manuscript: Base NarrowEps (prior standard deviation of 1‰ instead of 5‰ for all isotope effects) FixedEps (fixed instead of estimated isotope effects) Widerf (prior standard deviation of 100% instead of 25% for the contributions of anammox and DNRA) EnhBio (faster solute-difussion transport: Dbio = 2 cm2 d-1 instead of 1 cm2 d-1) AnamOff (switched off anammox: fAnam,Den2 = 0; fAnam,side = 0) DNRAOff (switched off DNRA: fDNRA1,Den1 = 0; fDNRA2,Den2 = 0) NitOff (switched off nitrification: kNit1 = 0; fNit1,Nit2 = 0) OneStep (one-step instead of three-step denitrification)