CEQUEAU is a process-based hydrological model capable of simulating river flows and temperatures. Despite an active user base, no facility yet exists for the automatic assembly and input of watershed data required for flow simulations. CEQUEAU can therefore be time-consuming to implement, particularly on large (≥104 km2) watersheds. We detail a new MATLAB toolbox designed to remove this key limitation by automatically computing CEQUEAU's key drainage direction and physiographic inputs from geographic information system (GIS) data. With the toolbox, model implementation can now be achieved extremely quickly (<1.5 hr) given suitable inputs. This time saving enabled us to assess CEQUEAU's sensitivity to changes in grid size by implementing the model on a large (14,990 km2) watershed at successively decreasing resolution (2.5 km to 112 km), using a fixed calibration parameter set. Results of this analysis showed that despite some model strength fluctuations linked to variability in computed basin size/land-use, only a minor decrease in model strength (mean Nash–Sutcliffe efficiency (NSE) reduction = 0.03) was observed at relatively fine resolutions (2.5 km to 20 km). Although results might change if the model was recalibrated at each resolution step, findings indicate that CEQUEAU is able to provide realistic flow simulations at a wide range of resolutions.