The effects of chlorination on 16 humic and fulvic acids (HAs and FAs, respectively) extracted from six different soil samples from Korea and two purchased soil samples (Canadian peat moss, Elliott Silt Loam Soil) were investigated to identify the changes in their structural characteristics and their effects on trihalomethane formation potential (THMFP) and haloacetic acid formation potential. The effect of chlorination was also investigated in fractionated samples (Aldrich HA, F1–F5) based on molecular weight (MW). Total organic carbon (TOC), specific UV absorbance (SUVA), fulvic-like fluorescence (%FLF), terrestrial humic-like fluorescence (%THLF), weight-average molecular weight (MWw), and carbon structures (13C NMR) were measured for each sample before and after chlorination, and factors relating to the chlorination mechanism were examined using principal component analysis (PCA). The results showed that the changes in the structural characteristics and the disinfection by-product formation of chlorinated HA and FA differed critically. For chlorinated HA, TOC and %FLF decreased due to oxidation, whereas %THLF was reduced via incorporation; MW also affected the structural changes and THMFP generation. In the PCA results, high SUVA, low MW, low N/C, and low O groups of aromatic C were associated with high THMFP production in HA, whereas low O groups of aliphatic C in FA were associated with both oxidation and incorporation in terms of THMFP. These results elucidate the mechanisms associated with the effects of chlorination in HA and FA and will support the prediction of THMFP generation in HA and FA based on their specific structural characteristics.