The goal of this study was to develop a reservoir model for the Aubonne karst watershed in the Swiss Jura using the systems approach. The Aubonne karst aquifer drains towards two main springs at different altitudes. Three models with different structures were evaluated for their performance. The best model was obtained by splitting the watershed into bands according to altitude and aspect in order to allow heterogeneous calibration. A double reservoir with outflows at different levels makes the repartition of discharge between the two springs possible. Our model was calibrated using discharge data from both springs and an additional downstream measurement station. A combined manual and automatic calibration approach based on a local search algorithm was applied. Validation over a 30 years period showed good agreement of the discharge data downstream of the springs.