Vertical mixing in the thermocline of lakes is poorly understood and most of the current knowledge is based on ex situ methods like laboratory measurements and simulations. Here we used the eddy correlation technique (EC) to directly measure oxygen and buoyancy fluxes in the thermocline of two lakes (Lake Scharmützelsee and Lake Arendsee in 2012 and 2013, respectively). Additionally, sets of temperature microstructure profiles (SCAMP) were measured during the EC deployments. We used these data to quantify the mixing efficiency as well as the turbulent diffusivity. The derived turbulent diffusivities from EC for the Prandtl number of DO were one order of magnitude higher than predicted by commonly applied parameterization, while the diffusivities for the Prandtl number of heat confirmed the parameterization. The results from EC and SCAMP showed strong differences which we attribute to the fact that SCAMP measurements reflect snapshots of the instantaneous turbulence field while EC provides a temporal average of the prevailing turbulence. Finally, we discuss problems of the EC and the inertial dissipation method in a strongly stratified environment and propose how they could be improved to resolve the full temporal variability of mixing in thermoclines.