The paper presents the results of studies on the influence of the 2010 Vistula flood on the humification process in the bottom sediments of the Goczałkowice Reservoir in southern Poland. Due to its location in the vicinity of farmlands, forests and urbanized areas, the Goczałkowice Reservoir is characterized by amplified and intense humification processes within its sediments. The studies were focused on the determining the influence of the flood wave containing organic and inorganic suspensions on these processes. Humic acids were analyzed using two spectroscopic methods: Electron Paramagnetic Resonance (EPR) and Fourier Transform Infrared Spectroscopy (FT-IR). Application of these methods allowed to determine the values of free radicals and of the g-factor, which are indicators of oxidation, aromatization and maturation of humic acids during the humification process, as well as the value of the 1650/1720 ratio, reflecting the dissociation of the COOH group to COO− and the formation of complexes of transitional metals with humic acids during the humification process.