A new approach, combining microwave digestion and sensitive determination of selenium by a normal-phase high performance liquid chromatography after derivatization with 2,3-diamino-naphthalene was proposed to the measurements of trace selenium concentration in natural waters. Two digestions systems, I.e. HNO3 and H2SO4-H2O2, were evaluated and their working conditions were optimized. Under optimal conditions, this approach provides a detection limit of 7.2 pg (with HNO3） or 10.4 pg (with H2SO4-H2O2）, a recovery of 99.1%～103.4%, as well as a linear range of 0～1.5 ng Se(Ⅳ). The approach was applied to determine Se concentration in 4 different types of environmental waters (sample volume: 2 mL) and the concentration levels of 0.20～0．90　μg/L were found, with recoveries of 99.1%～103．4% by standard addition.