The Yeongsan (YS) Reservoir is an estuarine reservoir which provides surrounding areas with public goods, such as water supply for agricultural and industrial areas and flood control. Beneficial uses of the YS Reservoir, however, are recently threatened by enriched non-point and point source inputs. A series of multivariate statistical approaches including principal component analysis (PCA) were applied to extract significant characteristics contained in a large suite of water quality data (18 variables monthly recorded for 5 years); thereby to provide the important phenomenal information for establishing effective water resource management plans for the YS Reservoir. The PCA results identified the most important five principal components (PCs), explaining 71% of total variance of the original data set. The five PCs were interpreted as hydro-meteorological effect, nitrogen loading, phosphorus loading, primary production of phytoplankton, and fecal indicator bacteria (FIB) loading. Furthermore, hydro-meteorological effect and nitrogen loading could be characterized by a yearly periodicity whereas FIB loading showed an increasing trend with respect to time. The study results presented here might be useful to establish preliminary strategies for abating water quality degradation in the YS Reservoir.