Dataset of O3 fluxes measured by the eddy covariance system over Lake Kuivajärvi during 23 days period in August and September 2012. The lake is located in the vicinity of the Hyytiälä Forestry Field Station and SMEAR II Station in Southern Finland. The dataset consists of post-processed and quality filtered fluxes and auxiliary measurements that were used in the analysis. The flux measurements were performed on the lake platform, by using an ultrasonic anemometer (Metek USA-1, GmbH, Elmshorn, Germany) to measure the three wind velocity components and sonic temperature and a fast chemiluminescent gas analyzer FOS (Sextant Technology Ltd, New Zealand) that measured O3 concentration.