The main goal of this work was to estimate the influence of carboxyl and phenolic groups, as well as aromatic, aliphatic and polysaccharide components, on the soil humic acids (HA) self-aggregation process. Soil HAs (leptosol and regosol) were separated using base resin getting fractions with different functional group contents. Blocking of carboxyl groups was performed using the esterification procedure to estimate the participation of each functional group in the HA aggregation. The presence of HA structural components was evaluated by potentiometric titration and ATR-FTIR. The aggregation was monitored at pH 3 using dynamic light scattering. Results indicated that the higher group content, the HA aggregation is less pronounced. A significant positive correlation of aliphatic C and aggregate size revealed their dominant influence in the HA self-aggregation. A lower abundance of aliphatic C in HA fractions could be considered as not sufficient to start the process. An increase of aromatic C in esters likely pointed out to its participation in hydrophobic bonding and, consequently, more pronounced aggregation. The relation of HA self-aggregate size with carboxyl and phenolic group, as well as aliphatic C, at low pH, could be considered universal regardless of the structural characteristics of the original or modified HA forms.