An automated continuous homogeneous microextraction approach based on a flow system has been developed and coupled with a hydride generation atomic fluorescence spectrometry system (HG-AFS). The developed approach was applied for the determination of trace arsenic and selenium in environmental water and liver samples. The nonanoic acid was investigated as a switchable hydrophilicity solvent (SHS) for homogeneous microextraction of As(III) and Se(IV) complexes with pyrrolidinedithiocarbamate (PDC). The procedure involved on-line mixing ammonium PDC (aqueous phase), sodium nonanoate (aqueous phase) and acid sample solution resulting in the formation of SHS (nonanoic acid) dispersed into the acid aqueous phase. By this continuous process, analytes complexes with PDC were formed and extracted into the fine SHS droplets followed by retention into a monolithic column packed with block of porous PTFE. Finally, the retained complexes were eluted with NaOH solution and delivered to the HG-AFS system. The limits of detection, calculated from a blank test based on 3σ were 0.01 μg L⁻¹ for both analytes.