This dataset resulted from a parallel monitoring at two lakes, Lake Tiefer See (near Klocksin, TSK; 53° 35.5’ N, 12° 31.8’ E; 62 masl; N Germany) and Lake Czechowskie (Jezioro Czechowskie, JC; 53° 52.4’ N, 18° 14.3’ E; 108 masl; N Poland), and includes four different type of data for both locations: (i) sediment cores microfacies data, (ii) sediment fluxes and composition, (iii) selected water column data, and (iv) selected meteorological information obtained on site. This dual lake monitoring set-up was established in 2012 with the aim to investigate seasonal sedimentation and varve forming processes in detail. The datasets are provided in individual *.csv files, per type of data and per lake. The thin section data from surface sediment cores comprises the thicknesses of the most recent calcite varves’ sub-layers: spring diatom sub-layer, summer calcite sub-layer, and autumn/winter re-suspension sub-layer. The sediment flux data was obtained from sediment traps located in different water depths (epi- and hypolimnion), and the sediment composition is given by the fluxes of total organic carbon (TOC), calcium carbonate (as calculated from total inorganic carbon; TIC), and diatoms & inorganic matter. The water column data comprises water temperature from stationary loggers, and dissolved oxygen measured in ~ 1 meter depth-resolution. The meteorological data includes daily averages of air temperature and mean wind-speed, and summed daily rainfall. Further details about the sampling and analytical methods, data acquisition, and processing are given in Roeser et al. (2021; http://doi.org/10.1111/bor.12506).