A pre-dredging investigation of the physico-chemical qualities of the River Niger at the Onitsha-Urban Stretch was undertaken between January 2008 and December 2009. With the exception of the downstream station I and upstream station 5 (stations with minimal perturbations), stations 2, 3 and 4 had colossal but varied degrees of domestic, industrial, agricultural and automobile waste deposits. Of the 26 physico-chemical parameters determined, Transparency, Total Alkalinity, Conductivity, Total Dissolved Solid (TDS), Total Suspended Solid (TSS), Total Solid (TS), Depth, Nitrate, Lead, Iron and Calcium varied significantly (P<0.01) among the stations. Aposteriori Duncan Multiple Range test showed that Transparency was significantly (P<0.001) higher at station 5 than at the other stations. Total Alkalinity and Conductivity were higher in stations 2 and 3, 1 and 4 than in station 5. TDS, TSS and TS were significantly higher at stations 2, 3, 4 than in stations 1 and 5. Air and water temperatures were significantly different (P<0.05) across the 5 stations while CO 2 was significantly higher at station 1 than others. pH in stations 2 and 5 is significantly higher than it is in 1, 3 and 5. DO was higher in station 5 and 2 than the other stations. BOD was highest in stations 1 and 4 than the other three stations. The principal Component Analysis using Varimax Rotation showed that the major parameters controlling the water quality of the study area were pH, air temperature, transparency, BOD, Dissolved Oxygen (DO), total alkalinity, conductivity, water current, phosphate and total dissolved solids (TDS).