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Abstract. Observed groundwater head and soil moisture profiles are assimilated into an integrated hydrological model. The study uses the ensemble transform Kalman filter (ETKF) data assimilation method with the MIKE SHE hydrological model code. The method was firstly tested on synthetic data in a catchment of less complexity (the Karup catchment in Denmark), and later implemented using data from real observations in a larger and more complex catchment (the Ahlergaarde catchment in Denmark). In the Karup model, several experiments were designed with respect to different observation types, ensemble sizes and localization schemes, to investigate the assimilation performance. The results showed the necessity of using localization, especially when assimilating both groundwater head and soil moisture. The proposed scheme with both distance localization and variable localization was shown to be more robust and provide better results. Using the same assimilation scheme in the Ahlergaarde model, groundwater head and soil moisture were successfully assimilated into the model. The hydrological model with assimilation showed an overall improved performance compared to the model without assimilation.