Many of the peatlands that used to extend over large parts of Northern Europe have been reclaimed for agriculture. Human influence continues to have a major impact on the hydrology of those that remain, affecting river flow and groundwater levels. In order to understand this hydrology it is necessary to analyze and assess the groundwater and surface water system as a whole. The SIMGRO model was developed for such situations: it simulates groundwater flow in the saturated and unsaturated zones and also surface water flow. Being physically-based, it is suitable for application to situations with changing hydrological conditions and for practical aspects of water management in peatlands. This paper describes the application of the model to different hydrological situations in the Netherlands, Poland and Lithuania. The 3 cases deal with aspects of flooding, natural flow regime and flood storage in relation to suitable conditions for agriculture and nature. The calibration of the model for the cases was limited, but the simulation results show that the estimates of the discharges and groundwater levels were satisfactory, demonstrating that the model is an adequate tool for simulating the hydrological system, and has the potential to assess the impact of different measures. The Dutch case demonstrates that lowland basins where the groundwater has been lowered by extensive land drainage can be restored by restricting the inflow of surface water from the upper parts of the basin: peak flows are significantly reduced. For the Polish case, the damming of ditches in the valley of the Biebrza River could significantly improve the water regime in the peatlands of this floodplain. For the Lithuanian case, the flow regime for the Dovine River could be made more natural if sluice gates were replaced by overflow spill weirs. Understanding the hydrological system is crucial for sustainable land development and effective soil and nature conservation. The different measures simulated in the 3 cases illustrate SIMGRO’s potential to simulate hydrological measures.