The data file is a matlab file (MATLAB 8.2) that contains structures providing the data used in the analysis of lake metabolism in Lake Illmensee, Germany. Data set comprises of: 1. Original time series on CO2, O2 and Temperature 2. Morphometric data on Lake Illmensee 3. Time series of derived data: a) atmospheric fluxes of CO2 and O2 b) vertical turbulent diffusivities c) mixing depth d) metabolic rates All structures provide detailed information on the data. The equations and models used can be found in the paper: Lake Metabolism: Comparison of lake Metabolic Rates Estimated from a Diel CO2- and the Common Diel-O2 technique in a manuscript submitted to PlosOne in 2016.