In this dataset, we present the initial soil parameters of two cores from a palsa and a peatland in Lapland, as well as hydro-chemical parameters of thermokarst water used for inoculating par of the mesocosms. We measured sedimentary and hydro-chemical parameters, along with the humification index obtained through FTIR analysis. The replicate cores were incubated under different water treatments to identify the effect of hydrological conditions on carbon mineralization.