Pharmaceuticals are emerging contaminants in the aquatic environments. Their presence poses toxicological effects in humans and animals even at trace concentrations. This study investigated the presence of antibiotics, anti-epilepsy and anti-inflammatory drugs in river water of selected rivers in the Eastern Cape Province in South Africa. Enzyme-linked immunosorbent assay was used for screening of sulfamethoxazole and fluoroquinolones antibiotics. The samples were collected in upper-stream, middle-stream and lower-stream regions of the rivers and effluent of selected wastewater treatment plants. Pre-concentration of the samples was conducted using lyophilisation and extraction was conducted using solid phase extraction (SPE) on Waters Oasis hydrophilic-lipophilic-balanced cartridge. The percentage recovery after sample clean-up on SPE was 103% ± 6.9%. This was followed by ultra-performance liquid chromatography electrospray ionization tandem mass spectrometry. The detected analytes were sulfamethoxazole, erythromycin, clarithromycin and carbamazepine. Carbamazepine and erythromycin were detected in high concentrations ranging from 81.8 to 36,576.2 ng/L and 11.2 to 11,800 ng/L respectively, while clarithromycin and sulfamethoxazole were detected at moderate concentrations ranging from 4.8 to 3280.4 ng/L and 6.6 to 6968 ng/L, respectively. High concentrations of pharmaceuticals were detected on the lower-stream sites as compared to upper-stream sites.