Interactions of mercury (Hg) with different molecular weight fractions of humic substances (HS) play an important role in controlling distribution, diffusion, speciation, and bioavailability of Hg in natural systems. This study suggests that Hg prefers to associate with higher molecular weight fractions of HS and this association particularly predominates at low pH and high ionic strengths of the medium. The concentrations of aggregated HS (with higher molecular weight) become high at lower pH (acidic condition) and high ionic strength. Molecular weight of HS gradually decreases with the increasing pH (basic condition) and low ionic strength of the medium. The disaggregation property of HS which involves the release of monomers from the surface of the aggregates produces HSs of different intermediate molecular weight with different Hg complexing capacity. Distribution of Hg in different molecular weight fractions of HS is dependent on aggregational and disaggregational properties of HS in aquatic medium. Association of Hg with high molecular weight fraction of HS may alter distribution and bioavailability of Hg in a system as the bioreactivity of organic matter decrease along a continuum of size in aquatic medium.