Selenium can either be essential or toxic depending on the concentration and oxidation state. In this study, the concentrations of inorganic selenium [Se(IV)] in water samples were determined in the presence of hexavalent selenium [Se(VI)} in water. Water samples were collected from ten different sampling sites in Blood and Mokolo Rivers in Limpopo Province, South Africa. A solid phase extraction (SPE) method with Dowex 1 × 2 resin (chloride form) as an adsorbent material was used to preconcentrate and separate Se(IV) selectively in the presence of Se(VI) in water samples. Concentrations of Se(IV) were quantified by inductively coupled plasma-mass spectrometry (ICP-MS) and ranged from 0.0411 to 0.820 µg/L and 0.135 to 2.79 µg/L in Blood and Mokolo Rivers, respectively. The presence of Se(IV) in water samples collected from Blood and Mokolo Rivers suggests that industrial and agricultural activities around these rivers have an impact on water quality.