Fixed-bed processes handling lignocellulose pose several challenges for reactor modeling. The fluid and solid material as well as the complete fixed-bed show varying properties with temperature, composition and advancing reaction progress. For this reason, biomass-specific reaction kinetics need to be combined with detailed heat and mass transfer, varying material properties and the filling process. In the present work, a detailed reactor model for hydrothermal flow-through pretreatment of pelletized wheat straw at 3 L scale is developed. For the first time, this model not only considers reaction kinetics and simple mass transfer equations but also heat transfer, non-ideal flow and varying fixed-bed properties during the filling process as well as the extraction phase. The influence of different levels of detail is discussed and the final model is validated at 185-215 degrees C with prediction accuracies between 0.013 and 0.02 kg/kg for hemicellulose oligomers and 0.0008 and 0.004 kg/kg for monomers.