Monitoring changes occurring in water bodies is a tool to make a sound decision on water quality management. This work investigates water quality parameters and metabolites in the Bloukrans, Buffalo, Swartkops and Tyhume Rivers in the Eastern Cape Province of South Africa. The water physicochemical parameters assessed include the dissolved oxygen, oxidation-reduction potentials, temperature, Hydrogen ion concentration, salinity, conductivity, turbidity and total dissolved solids measured with a pre-calibrated Hanna Multiparameter instrument on-site. Chemical oxygen demand, phosphate, chloride, ammonium, sulphate and nitrate ions were measured in the laboratory with a UVmini spectrophotometer. FT-IR analysis of extracted metabolites was done on a Perkin Elmer FT-IR spectrometer. The result shows that upstream river samples have lower COD values and below the detection level in some. The concentrations of phosphate, chloride, ammonium, sulphate and nitrate ions were above the recommended values in the wastewater effluents, midstream and downstream river samples. FT-IR peaks similar to vinylidene, saturated aliphatic aldehydes, aryl aldehydes, primary amines, hydantoin amides, halogen, and organofluorides were common in the wastewater effluent samples and the receiving rivers. Grahamstown treated wastewater effluents and its receiving Bloukrans River were distinguished with absorption peaks of urethane and aromatic aldehydes. Absorption peaks of sulphonyl halides were present only on the spectra of treated wastewater effluents of Alice and the receiving downstream Tyhume River. Multivariate analysis shows correlations between the water samples from different geographical locations and treated wastewater effluents. It is concluded that the quality of the rivers was very poor and more efforts are needed to make the treated wastewater conform to the acceptable standard for a sustainable aquatic ecosystem.