Prompt gamma neutron activation analysis (PGNAA) technology is used in heavy metals measurement. It is found that the detection accuracy of lead (Pb) is impacted heavily by mercury (Hg), because of thermal neutron cross section of mercury is much bigger than lead. In this paper, a new combined detection method was proposed to improve the lead measurement accuracy in situ environmental water rejects analysis by PGNAA-XRF. Thus, a combined measurement facility was developed to analyze the mercury and lead in water simultaneously. The geometry of set-up is determined by a series of simulations with the MCNP code to improve the detection efficiency of the prompt gamma-ray intensity (Iγ) and characteristic X-ray fluorescence intensity (IX) of element. The ideal sample height and cavity are 33 and 16 cm, respectively. The influence of the relationship between Iγ, IX and different concentration (ｃi) of Hg and Pb was researched by MCNP calculations, respectively. The simulation results showed that there were good linear relationships between Iγ, IX and ｃi, respectively. The empirical formula of combined detection method was proposed based on the above calculations. The limits of detection for Hg and Pb with the combined measurement instrument were 3.89 and 4.80 mg·kg-1, respectively. It is a significant increase in performance of the mercury and lead detection simultaneously.