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In this study, we investigated the interrelationships between organic matter and water quality indices in the total maximum daily load basins, namely, Churyeongcheon and Yocheon of the Seomjin River system, and identified trends. Churyeong A and Yocheon B, the basins being analyzed, have high proportions of nonpoint pollution sources and pollutant loads from terrestrial sources. During the study period, biochemical oxygen demand (BOD) decreased in both basins, whereas chemical oxygen demand (COD) and total organic carbon (TOC) increased in Churyeong A and decreased in Yocheon B. The increase in organic matter in Churyeong A correlated with the flow rate, whereas organic matter in Yocheon B showed little correlation with flow rate. Variations in organic matter (BOD, COD, and TOC) in Churyeong A exhibited seasonality under the influence of increased flow rate. Organic matter in Yocheon B was affected by increased flow rate, wherein with time, BOD decreased and COD and TOC increased. This study provides basic data that can be used as a reference to facilitate continuous water management and appropriate strategy implementation by analyzing the influencing factors and trends of organic matter using long-term measurement data. [ABSTRACT FROM AUTHOR]