The purpose of this study was to compare the molecular size distribution (MSD) of natural organic matter (NOM) in raw waters (RW) and drinking waters (DW), and to find out the differences between MSD after different water treatment processes. The MSD of NOM of 34 RW and DW of Finnish waterworks were determined with high-performance size-exclusion chromatography (HPSEC). Six distinct fractions were generally separated from water samples with the TSK G3000SW column, using sodium acetate at pH 7 as an eluent. Large and intermediate humic fractions were the most dominant fractions in surface waters (lakes and rivers), while in artificially recharged groundwaters and natural groundwaters intermediate and small fractions predominated. Water treatment processes removed the two largest fractions almost completely shifting the MSD towards smaller molecular size in DW. Granular activated carbon (GAC) filtration, ozonation, and their combination reduced all humic fractions compared to the conventional treatment. Humic fractions correlated with total organic carbon (TOC) content and chemical oxygen demand, this being especially true in RW. The results demonstrate that the HPSEC method can be applied for a qualitative and also for rough estimate quantitative analyzes of NOM directly from RW and DW samples without sample pretreatment.