Studies have shown that humic substances in soil organic matter have various functionalities. In this study, we focused on water-soluble organic components, such as dissolved organic matter (DOM), and applied the method proposed by Tsuda et al. (2016), which has been used to analyze water-extractable humic substances (WEHS) in DOM in lakes, to soil samples for the first time to quantify WEHS in farmlands. The amount of WEHS in agricultural soils in Kanagawa Prefecture was found to be proportional to the amount of water extracted organic matter (WEOM) for the first time in this study. The amount of WEOM was generally higher in the crop layer than in the next surface layer immediately below the crop layer; the same trend was observed for WEHS. The amount of WEHS in WEOM varied greatly among various study sites. However, the percentage of WEHS showed a strong positive correlation between the cultivated and next surface layers. These results indicate that the total amount of soil organic matter influences the amount of WEOM and the amount of WEHS in WEOM. Moreover, the nitrogen in WEOM was found to be mainly present in non-WEHS and almost WEHS. The high positive correlation between the amounts of carbon and nitrogen in WEHS shows that the nitrogen compounds present in WEHS are chemical structures that are constrained to some extent.