The separation of selected lignin/humic substance (HS) degradation compounds by capillary electrochromatography (CEC) with a methacrylate-based monolithic column and a conventional column packed with 5 microm octadecyl silica (ODS) particles is presented. The effects of organic modifier concentration, pH of the mobile phase, ionic strength, applied voltage, and temperature on the separation were investigated to determine the optimal separation conditions. With the increase of pH in the mobile phase, some of analytes start to ionize and both chromatographic partition and electrophoresis can play roles in separation simultaneously. Accordingly, different selectivity from high-performance liquid chromatography (HPLC) and capillary electrophoresis (CE) could be achieved. The performances of both kinds of columns were compared. The results showed that the peaks of compounds obtained on the former column were much wider than those on the latter one, although good separation efficiency of alkylbenzenes could be readily achieved; the most probable reasons for this behavior and method to solve this problem were briefly discussed. The CEC of a soil fulvic acid with a monolithic column produced partly resolved broad bands; by means of nuclear magnetic resonance (NMR) analysis a wide range of oxygen derived aromatic substitution patterns was found with prominent contributions from phenolic and carboxylic groups.