Most catchment modelling software use a Graphical User Interface (GUI) to support model applications. A GUI is generally user-friendly for novice users but opens sources of irreproducible research. We illustrate this risk by showing that none of the 10 Soil and Water Assessment Tool (SWAT) studies over the Upper Blue Nile Basin report all settings required to reproduce the model results. We present a workflow (QSWAT Workflow) that promotes reproducibleSWAT model studies while remaining user-friendly for both novice and expert users. The workflow creates a SWAT model based on namelist file while maintaining GUI compatibility. We applied the workflow to the Blue Nile catchment and show that it yields the same results as QSWAT GUI. We conclude that such user-friendly workflows can help reduce cases of irreproducible catchment studies and offer opportunities for increased transparency and reusability of hydrological models. The workflow is publicly available on https://github.com/VUB-HYDR/QSWAT_Automated_Workflow