Water qualities of Lake Sanaruko and Teganuma in Japan have had the worst COD value of all the lakes in Japan over the past several years. In this study, the pollution mechanisms active in two lakes were studied by analyzing the data of aqueous environmental samples. It was observed that SS (Suspended Solid)-COD values correlated with Chl.a (Chlorophyll a) concentrations, which represent the population density of phytoplankton, and the growth of phytoplankton was accelerated by eutrophication in the lakes. Although Chl.a concentrations had some variations because the species of dominant phytoplankton vary seasonally, the COD values remained constant almost all year round, which suggested that the generation of phytoplankton occurs constantly, regardless of the temperature or season. The influent rivers mainly supply nitrogen and phosphorus, which caused eutrophication in both lakes. By comparing their average concentrations in the lake and in the rivers, it was presumed that the decrease of nitrogen concentration might occur by denitrification in both lakes; whereas, phosphorus might be released in small quantities from the bottom of both lakes. It was observed that the ratio of particulate matter SS-COD/Organic-N/Organic-P in both lakes had remained nearly constant, and that the concentration of phosphorus in the influent rivers had continued to decrease in Lake Sananruko. From these results, it is expected that the total COD will reach 5 mg/L after eight years in this lake. If the lake purification projects can be carried out more quickly, water quality will improve earlier than expected.