This study developed an efficient management plan to improve the water quality by analyzing fluctuations in the ratio and amount of various organic substances in streams considering watershed characteristics and rainfall patterns. Monitoring was conducted on three streams and one lake over seven sessions during wet and dry seasons. Water quality indicators including total organic (TOC), refractory dissolved organic (RDOC), and particulate organic (POC) carbons were analyzed using high-temperature combustion oxidation. The three streams (Cheongmi, Yanghwa, and Bokha) displayed high TOC concentrations during the rainy season because the accumulated organic substances from the dry season were washed away by rainfall. By contrast, Paldang Lake exhibited a substantial decrease in TOC concentration due to dilution, which was influenced by watershed and rainfall characteristics. Across all streams and lakes, dissolved organic carbon (DOC) accounted for the highest proportion, at 77.5% of TOC, with RDOC making up 91% of DOC and 71% of TOC. Although POC contributed a small annual proportion to annual TOC, the concentration rapidly increased during late spring and early summer, with increases of 40.403%, 25.99%, and 27.388% in Cheongmi, Yanghwa, and Bokha, respectively. Continuous monitoring of RDOC is essential to identify seasonal fluctuations and changes due to rainfall events. Furthermore, intensive POC management during the rainy season, particularly in May and June, is potentially economical and efficient for water quality management.