In the present paper, a new combined detection method was proposed using prompt gamma neutron activation analysis (PGNAA) and characteristic X-ray fluorescence to improve the heavy metals measurement accuracy for in-situ environmental water rejects analysis by PGNAA technology. Especially, the characteristic X-ray fluorescence (XRF) of heavy metals is induced by prompt gamma-ray directly instead of the traditional excitation sources. Thus, a combined measurement facility with an 241Am-Be neutron source, a BGO detector and a NaI-Be detector was developed to analyze the pollutants in water. The two detectors were respectively used to record prompt gamma-ray and characteristic X-ray fluorescence of heavy metals. The prompt gamma-ray intensity (Iγ) and characteristic X-ray fluorescence intensity (IX) was determined by MCNP calculations for different concentration (ci) of chromium (Cr), cadmium (Cd), mercury (Hg) and lead (Pb), respectively. The simulation results showed that there was a good linear relationship between Iγ, IX and (ｃi), respectively. The empirical formula of combined detection method was given based on the above calculations. It was found that the combined detection method was more sensitive for high atomic number heavy metals like Hg and Pb measurement than low atomic number like Cr and Cd by comparing and analyzing Iγ and IX. The limits of detection for Hg and Pb by the combined measurement instrument were 17.4 and 24.2 mg·kg-1, respectively.