To understand how forest harvest influences the aquatic environment, it is essential to determine the changes in the flow regime. This paper presents changes in the hydrological regime during the first 2 y after harvest in two catchments of the Balsjö Catchment Study in Sweden. The changes were judged relative to a reference catchment, calibrated during an 18-mo pretreatment period starting in September 2004. From August 2006 through March 2008, there was an average of 35% more runoff from the harvested catchments relative to the reference. The flow increased most during the growing seasons and at base flows (<1 mm d−1; 58–99% increase), followed by dormant season and intermediate flows (30–43%). No significant changes were observed during the highest flows (over 5 mm d−1), except for the spring flood a few weeks after harvest, which was delayed and attenuated. Large relative changes in low flow may influence the ecosystem by altering the aquatic habitat.