Here, we present data of chemical oxygen demand, biochemical oxygen demand and dissolved organic carbon conducted from our measurements and collated from literatures. These data cover a wide variety of natural aquatic environments ranging from tropical to subarctic zones, farmlands to forest watersheds, high plateaus to coastal waters, and freshwaters to saline lakes and marine waters. We also provide four ultra-high resolution mass spectrometry data files showing dissolved organic matter in the river water samples before and after 510 days incubation, and remaining organic matter of these two samples after chemical oxygen demand treatments. In addition, long-term data on chemical oxygen demand and biochemical oxygen demand in Lake Biwa in Japan, the Han River in Korea, and Finnish rivers are also presented.