A hydrophilic interaction liquid chromatography (HILIC) method was developed to measure the composition of humic substances from river, reservoir, and treated wastewater based on their physicochemical properties. The current method fractionates the humic substances into four well-defined groups based on parallel analyses with a neutral and a cationic HILIC column, using mobile phases of varied compositions and pH. The results indicate that: (i) the proportion of carboxylic acids in the humic substances from terrestrial origins is less than half of that from treated wastewater (Jeddah, KSA), (ii) a higher content of basic compounds was observed in the humic substances from treated wastewater and Ribou Reservoir (Cholet, France) than in the sample from Loire River (France), (iii) a higher percentage of hydrophobic macromolecules were found in the humic substances from Loire River than in the other samples, and (iv) humic substances of treated wastewater contained less ionic neutral compounds (i.e., pKa 5-9) than the waters from terrestrial origins. The physicochemical property disparity amongst the compounds in each humic substances sample was also evaluated. The humic substances from the lightly humic Loire river displayed the highest disparity, whereas the highly humic Suwannee river (Georgia, USA) showed the most homogeneous humic substances.