The aim of this study was to clarify the impact of differences between historical and recently introduced irrigation and drainage management systems on water quality in the rivers around paddy fields. We investigated the seasonal variation in nutrients concentration and dissolved organic carbon (DOC) components in single- (used for intake only) and dual-purpose (used for both intake and drainage) channels during a 4-year period in the Himi region of Toyama, Central Japan. The system of dual-purpose channel has traditionally been used in the region of this study. A total of 197 three-dimensional excitation-emission matrix (3DEEM) fluorescence spectra of DOM in waters were applied for the parallel factor analysis (PARAFAC) modeling. Based on the 3DEEM and PARAFAC, the abundance of terrestrial humic-like components in the dual-purpose channel was significantly higher than that in the single-purpose channel. The even long-chain n-fatty acids derived associated with rice cropping in sediments of the dual-purpose channels were 22−30-fold higher than that of the single-purpose channel. In addition, the turbidity values of the river waters had significantly positive linear correlations with concentrations of K+, DOC, and humic-like components. These observations indicate that the dissolved nutrient concentrations in the river water were higher in the dual-purpose channel compared to those of the single-purpose channel, which may be supplied by leaching from the inflow of soil particles from the paddy fields. During the mid-irrigation period, the quantity of epiphytic chlorophyll a on artificial substrate tiles in the dual-purpose channel were 3.1–4.1-fold higher than that in the single-purpose channel. This study clear that the input of paddy drainage during the irrigation season significantly changes the DOC components in river waters and irrigation management is strongly linked to the primary production in agricultural channels. Therefore, it is important to consider the impact of the introduction of different irrigation and drainage management systems on water quality and productivity in order to maintain the riverine ecosystems around rice paddies, which are based on historical water use systems.