Interest towards continuous cover forestry (CCF) has grown in recent years as it is considered more favorable from environmental perspectives than even-aged management. CCF could be particularly feasible on peatlands and other lowland soils as continuously maintaining a tree cover with significant evapotranspiration capacity could decrease the need for artificial drainage. Clear cutting, site preparation, and regular cleaning of drainage ditches increase greenhouse gas emissions and affect water quality by releasing sediment, nutrients and carbon to water bodies. Whereas even-aged management on peatlands relies on these intensive and environmentally adverse practices, regeneration in CCF forests would occur naturally and evapotranspiration of the tree stand would play a key role in maintaining drainage conditions. Partial harvest is an essential component of CCF and our study focuses on understanding its impacts on hydrology. The study site comprises a fertile drained peatland forest in Southern Finland, where three parallel sites were established in March 2016: (i) clear-cut with site preparation and seedling planting, (ii) partial harvest removing 75% of tree biomass, and (iii) control left untouched as reference. Data on ecosystem fluxes (Eddy covariance) and ground water depth were available from each site after the harvest and for a pre-treatment period of 6 years. In our attempt to understand the mechanisms behind observed changes after clear-cut and partial harvest, we applied a one-dimensional multi-layer multi-species soil-vegetation-atmosphere transfer model in conjunction with data analysis. The hydrology of each parallel site was simulated to explore the role of the amount and diversity of vegetation. Results suggested that on the partial harvest site the undergrowth of birch and spruce had the potential to partly compensate for the transpiration of the harvested pine, which dominated the stand before the treatment and limited the light received by the undergrowth trees. Such changes in vegetation-driven water balance components revealed by mechanistic modeling form the basis for understanding vegetation controls on growing season ground water depth, which is a key factor for the successful implementation of CCF in peatland forests.