The effect of organic modifiers (organic solvents and urea) on the electrophoretic buffer was investigated in an attempt to enhance resolution in the finger-printing of two humic substances (HS): an aquatic fulvic acid (FA) and a soil humic acid (HA). Two detection modes, photodiode array and laser-induced fluorescence, were applied. The addition of organic solvents (acetonitrile, acetone, 2-propanol and tetrahydrofuran) in 10 mM Na2B4O7 (pH 9.0) resulted in a clear difference in electrophoretic behavior of the studied HS compared to the absence of organic solvents. There were also marked differences in the electrophoretic profiles using a 2-propanol-borate buffer with urea. The study of the interaction between metals and HS showed that there was a change in the migration pattern in the presence of A1(III), indicating the specific binding sites of aluminum.