The impact of controlled drainage (CD) on the groundwater table (GWT), drainage outflow, surface runoff, and nitrogen reduction at the drainage system scale in the Wielkopolska region was analyzed in this study. Based on field research, mainly by monitoring of GWT changes in 2019–2020, the DRAINMOD model was calibrated and validated. Hydrological soil water balance simulations were carried out with 36 and 9 combinations for CD and free drainage (FD), respectively. The modelling period was March-September for 10 different dry, wet, and normal years from the period of 1961 to 2020. The next step was to use the results of drainage outflow modelling and chemical constituent analyses of drainage water samples to determine NO3-N concentrations and calculate NO3-N pollution loads. As a result of the simulations, the importance of the timing of the start of the outflow retention in the adopted model variants was determined, indicating the earliest assumed date of 1 March. The appropriate CD start date as well as the initial GWT has a significant impact on the effectiveness of CD application in reducing the volume of drainage outflow and reducing the amount of NO3-N entering open water with it. The application of CD under the conditions of the analyzed drainage facility makes it possible to retain up to 22 kg of NO3-N per hectare.