Aquatic humic substances (AHSs) are major constituents of dissolved organic matter (DOM) in freshwater bodies. We performed quantitative analyses of AHSs in Japanese lake and wetland waters, focusing mainly on clear waters with low carbon contents, by using a resin isolation technique based on the carbon concentration in the AHSs of each sample. The proportion of AHS to DOM in the clear waters ranged from 38.4 to 64.1 %; these proportions are lower than those widely assumed for freshwater of 20-80 %. Moreover, the proportions of AHSs in DOM were not constant, so regression analysis cannot be used to predict the AHS concentration from the DOM concentration. Thus, AHS and DOM concentrations must be determined separately for each water sample.