Recent investigations provide new insight on the structural chemistry of dissolved organic matter (DOM) in freshwater environments and the role of these structures in contaminant binding. Molecular models of DOM derived from allochthonous and autochthonous sources show that short-chain, branched, and alicyclic structures are terminated by carboxyl or methyl groups in DOM from both sources. Allochthonous DOM, however, had aromatic structures indicative of tannin and lignin residues, whereas the autochthonous DOM was characterized by aliphatic alicyclic structures indicative of lipid hydrocarbons as the source. DOM isolated from different morphoclimatic regions had minor structural differences.