Fluorescence measurements on selected polycyclic aromatic hydrocarbons were performed to obtain the information about the fluorescence quenching of polycyclic aromatic hydrocarbons by humic acid. The fluorescence properties of pyrene and fluoranthene in the presence of humic acid in water were investigated by three dimensional excitation-emission matrix fluorescence spectroscopy. The pH influence on the fluorescence quenching of pyrene and fluoranthene were also investigated. For both pyrene and fluoranthene, the fluorescence quenching were dominated by static quenching processes. According to the result of the research, the effect of humic acid on the pyrene and fluoranthene can be calibrated in the water environment. The results show that three dimensional excitation-emission matrix fluorescence spectroscopy has great potential for the use of in-situ measurement of polynuclear aromatic compounds in water environment.