Interest in aspects of industrialization relating to human health has increased. Accordingly, the use of labels such as ‘natural foods’ and ‘organic ingredients’ has become more widespread, and greater emphasis is being placed on improving qual-ity of life. Water is an essential element for human life, and water quality has a significant impact on human health. However, technology that can precisely determine the substances present in water is still lacking. This study was conducted to establish a complete mass spectrometry process, from pretreatment to analysis, to measure and characterize natural organic matter (NOM) in Korean spring water samples. Salts and other matrices were removed from the samples using solid-phase extraction (SPE) with two different columns (PPL and C18). After establishing an accurate analysis method, the experimental results were evaluated based on Van Krevelen diagrams and analysis of molar O/C and H/C ratios. The method for characterizing NOM introduced herein should facilitate evaluation of water quality.