The Environmental Ministry of Schleswig-Holstein (Northern Germany) has implemented a novel peatland rehabilitation programme to utilise the high denitrification potential of degenerated, minerotrophic peatlands for the reduction of nitrate input into aquatic ecosystems, and to simultaneously improve the habitat conditions. Realisation of both goals requires changes to the water management adapted to the site-specific geohydrological conditions. The effect of raised groundwater levels and extensive land use on the water quality of heavily vegetated and groundwater-fed ditches was investigated in a riparian peatland located in the River Eider Valley (a nationally important wetland case study area). The water quality of the selected representative ditches was regularly assessed at different discharge levels during different flow obstruction cover periods. The hydraulic residence time was predominantly a function of the ditch geometry and the overall flow obstruction. A better understanding of the effect of ditch vegetation on the temporal flow patterns and the hydraulic residence times is of high environmental interest, especially for improving nutrient standards in lowland rivers such as the River Eider. Within-ditch vegetation and other hydraulic flow obstructions such as accumulated silt and organic debris increased the hydraulic residence time and led to an improvement of the water quality (e.g. reduction in nitrate content) along the ditch. While ortho-phosphate and ammonia concentrations were acceptable to German water quality standards, nitrate-nitrogen concentrations were frequently elevated due to high discharges despite high flow obstruction cover. Further findings show that the lower stretches of the ditches were flooded by the River Eider due to the absence of a macrophyte-mowing scheme that led to increased water levels during late summer.