Aquatic humic substances are amorphous organic macromolecules and precursors of mutagens formed on chlorination of raw water. Their isolation from River Mornos and Lake Yliki (primary reservoirs of Athens Water Supply and Sewerage Company) using columns of XAD-8 and IR-120 resins is performed in order to study their structural differences among reservoirs. Fractionation into humic and fulvic acids (HA and FA respectively) and spectroscopic examinations with FTIR technique is applied. In addition, THMFP is determined in every fraction of the reservoirs mentioned above. The presence of carboxylic acids and other functional groups such as alcohols, aromatic rings and aliphatic chains is indicated. Chloroform and chloropropanones detected can be considered to be products of humic acid, as they can be formed during chlorination of hydroxy-benzoic acid and beta-keto-carboxylic acid. The chlorosubstituted acetonitriles detected are attributed to the reaction between chlorine and aminoacid.