By evaluating and optimizing instrument parameters, mass spectral interferences, selection of selenium isotopes, the concentration of NaBH4 , the acidity of samples, Se(Ⅵ) reduction conditions and the hydride generation interferences, a method was developed for measuring inorganic selenium speciation in natural water by sector field inductively coupled plasma mass spectrometry combined with laboratory made continuous-flow hydride generation, which overcame the hydride generation interference from various elements in the natural water and resolved the problem that Se(Ⅵ)reduction behavior was various in different matrix and the time of remaining stable reduction recovery was short. The detection limit was 0. 002 μg/L and the sensitivity was 215378 cps/(μg/L) which were superior to that of other similar methods. The precision of Se(Ⅵ) and Se(Ⅵ) in river water and seawater was lower than 4%, and the spiked recovery ranged from 97% -103%. Thus, the proposed procedure was a suitable method for determining the Se(Ⅵ)and Se(Ⅵ)concentration in natural water including seawater, saline water, river water and so on.