Lowland areas are characterized by specific properties, such as flat topography, low hydraulic gradients, shallow groundwater, and high potential for water retention in peatland and lakes. These characteristics and their dominating hydrological processes have to be assessed and considered for the analysis and modelling of water balances in lowland catchments. The capabilities and challenges of modelling hydrological processes and water balances in mesoscale lowland river basins with the SWAT model are presented. The investigated catchments Stör, Treene and Kielstau are located in northern Germany within a lowland area. Covering areas from 50 to 517 km 2 , these rural meso-catchments have sandy, loamy and peaty soils. Drainage, in terms of tile drainage and open ditches, has changed the natural water balance. The set-up and modifications of the model as applied in these case studies can be transferred to other similar catchments in lowland areas. The dominating hydrological processes were found to be mainly controlled by groundwater dynamics and storage, drainage, wetlands and ponds. Some groundwater parameters were found to be highly sensitive and they turned out to be the most influential factors for improving simulated water discharge.