Carbon and nitrogen dynamics in the Sea of Japan (SOJ) are rapidly changing. In this study, we investigated the carbon and nitrogen isotope ratios of particulate organic matter (δ13CPOM and δ15NPOM, respectively) at depths of ≤ 100 m in the southern part of the SOJ from 2016 to 2021. δ13CPOM and δ15NPOM exhibited multimodal distributions and were classified into four classes (I–IV) according to the Gaussian mixed model. A majority of the samples were classified as class II (n = 441), with mean ± standard deviation of δ13CPOM and δ15NPOM of –23.7 ± 1.2‰ and 3.1 ± 1.2‰, respectively. Compared to class II, class I had significant low δ15NPOM (-2.1 ± 0.8‰, n = 11), class III had low δ13CPOM (-27.1 ± 1.0‰, n = 21), and class IV had high δ13CPOM (-20.7 ± 0.8‰, n = 34). All the class I samples, whose δ15NPOM showed an outlier of total data sets, were collected in winter and had comparable temperature and salinity originating in Japanese local rivers. The generalized linear model demonstrated that the temperature and chlorophyll-a concentration had positive effects on δ13CPOM, supporting the active photosynthesis and phytoplankton growth increased δ13CPOM. However, the fluctuation in δ15NPOM was attributed to the temperature and salinity rather than nitrate concentration, which suggested that the δ15N of source nitrogen for primary production is different among the water masses. These findings suggest that multiple nitrogen sources, including nitrates from the East China Sea, Kuroshio, and Japanese local rivers, contribute to the primary production in the SOJ.