Water quality parameters (pH, salinity, DO, BOD, total suspended solid (TSS), Total dissolved solids (TDS), Total hydrocarbon (THC), water temperature, heavy metals and rainfall) were analyzed from surface water samples collected at Okoro River estuary, Southeastern Nigeria between April 2011 to March 2013. Principal component analysis (PCA) was used in the ordination of physicochemical parameters. The results of the scree plot and eigenvalue decomposition, revealed five significant factors that explained> 75% of the total variance in the complex data set with their eigenvalues> 1. The structural resonance of the factor loadings (eigenvectors) followed a decreasing order of hydrological factors (35.30%), oil pollution (16.90%), dissolved salts (12.39%), natural mineralization (8.69%) climatic factors (6.89%) as the major factors responsible for the modification of the surface water quality of the area. This study recommended that PCA is a useful tool for identification, characterization and evaluation of water quality.