This paper delivers two issues: water quality in the Yeongsan (YS) watershed which is one of the major watersheds in Korea and new watershed management plans with respect to the total maximum daily loads (TMDL) management. Field studies were conducted to estimate the pollutant loads according to the spatial and temporal distribution based on the biochemical oxygen demand (BOD) concentration and the volumetric flow rate (VFR) data from YS watershed. The results of both spatial and temporal analyses show the main pollutant source was originated from the city of Gwangju and the pollutant load from the city to YS watershed was the most out of five cities during this study period. Concerning YS reservoir located downstream of YS watershed, it also shows the worst water quality in the entire watershed during the study period. These results collectively demonstrate that the city of Gwangju is a main region which generates numerous point and non-point pollutant sources and eventually the pollutants are accumulated in YS reservoir. Based on the results, we suggest two different management plans for YS watershed. One is the flow-control approach that is to increase the amount of dam discharge in order to guarantee the river management flow for the midstream region. The other is the mass-control approach that is to dredge the contaminated sediments in YS reservoir for removing pollutants chronically accumulated in the sediment. Simulations for the former and the latter provide the pollution mitigation rate in the watershed up to 6 and 8% for BOD5, respectively. The methodology proposed here for TMDL management can be applied to a wide range of watersheds in Korea.