Physical and chemical structure affect properties of dissolved organic matter (DOM). Recent observations revealed that heating and cooling cycles at higher temperature amplitude lead to a change in DOM physical conformation assumingly followed by a slow structural relaxation. In this study, changes at lower temperature amplitudes and their relation to DOM composition were investigated using simultaneous measurements of density and ultrasonic velocity in order to evaluate the adiabatic compressibility, which is sensitive indicator of DOM structural microelasticity. Six fulvic acids (FAs) having various origins were analyzed at concentrations of 0.12, 0.6 and 1.2 g L and at different temperature amplitudes. First, we validated that the used technique is sensitive to distinguish conclusively the structural changes upon heating and cooling of DOM with heating/cooling amplitude of ± 3 °C and higher. This amplitude was then applied to observe the relationship between change in adiabatic compressibility and chemical composition of FA. No correlation was observed with elemental composition and aromatic structures. Positive correlations were observed with content of alkyl moieties, carboxylic and carbonyl carbons and biological activity. Based on literature data, it was concluded that alkyl moieties undergo (re)crystalization during thermal fluctuation and their structural relaxation back is very slow (if occurs). The polar moieties form a flexible hydrogel responding to thermal fluctuation by moderate dissolution and re-aggregation. Negative correlation was observed in relation to the amount of peptide and O-alkyl systems, which can be attributed to very fast structural relaxation of proteinaceous materials, i.e. their larger content leads to lower difference between original and heat-induced compressibility. Last, the increase of the heating/cooling amplitude from ± 3 to ± 15 °C resulted in an increase of the change of the adiabatic compressibility and in the extension of the relaxation time needed for DOM structure to return to the equilibrium. We conclude that this increase is caused by the increase in inner energy, and DOM conformation can reach a cascade of energy minima, which may influence DOM reactivity and biodegradability.