Selenium is an important micronutrient for the human body, but biological concentrations on either side of its narrow nutritional window can lead to serious health impacts. Furthermore, Se(IV) has been reported to be more toxic than Se(VI). Therefore, prudent control and monitoring of Se intake should involve speciation of this element. Herein, the development and validation of an automatic sequential injection analysis (SIA) system and method for the speciation of Se(IV) and Se(VI) in water samples is reported for the first time. This method is based on the starch-iodide reaction using Se(IV) as the oxidant, which subsequently forms a blue compound with starch. Total selenium is determined after an online pre-reduction of Se(VI) to Se(IV) with HCl at 75 °C. The concentration of Se(VI) is then calculated as the difference between the total Se and Se(IV) concentrations. The calibration curves for Se(IV) and total Se are characterised by linear ranges of 0 – 1.5 mg L-1 and 0 – 2.5 mg L-1, limits of detection (LODs) of 0.02 mg L-1 and 0.07 mg L-1, and averaged relative standard deviations (RSDs) (n = 3) of 1.33 % and 2.95 % respectively, with a sampling rate of 10 h−1. The newly developed SIA method has been successfully applied to drinking water samples spiked with both Se species and good recoveries in the range 94 – 109 % have been achieved.