The photochemical generation technique of mercury vapor (PCVG) coupled with headspace solid phase microextraction (SPME) and microwave induced plasma optical emission spectrometry (MIP-OES) has been developed and successfully applied for fast and sensitive determination of mercury in complex matrix samples. Mercury vapor was generated by UV photo-reduction of inorganic mercury and methylmercury to mercury vapor in 5% (v/v) formic acid with subsequent gas-liquid separation and preconcentration by solid phase microextraction. A stopped-flow mode of the PCVG-SPME unit was employed with the aim of increasing analyte preconcentration factor, thus improving both sensitivity of determination and detection limits for mercury. The calibration curves were linear up to 20 ng mL−1 with the limit of detection for inorganic mercury and methylmercury of 0.030 and 0.045 ng mL−1, respectively. This manifold allowed a repeatability, expressed as relative standard deviation, of below 5%. Due to differences in efficiency of Hg vapor generation for Hg2+ and CH3Hg+, the quantification was performed against external Hg2+ and CH3Hg+ aqueous standards, respectively. The method was validated by the analysis of two CRM materials of different matrix composition, i.e. estuarine sediment ERM CC580 for total mercury content and tuna fish ERM CE464 for methylmercury content, respectively. The results proved good accuracy of the method with recovery of 101% total mercury and 87.3% methylmercury and precision of 3.8% and 12.5%, respectively. Effect of concomitants in the stopped-flow generation of mercury vapor with the new manifold was also investigated. Next, the proposed method was successfully applied for monitoring of bioaccessible fraction of mercury during their incubation in simulated body fluid in the presence of selenium nanoparticles examined as a potential mercury detoxifying agent.