Once chlorophyll molecules within the planktonic algae cells absorb light energy, they will release energy in the form of chlorophyll fluorescence emission. The elastic scattering light of particles in water is partially polarized, while chlorophyll fluorescence is unpolarized, so we can use the properties to separate the fluorescence signal from total scattering spectra for further retrieval the concentration of chlorophyll. But for coastal waters, the approach feasibility is still unclear. Based on this, we conducted the experiment in laboratory to analyze the influence of different concentrations of inorganic particles (IOP) and chlorophyll on the fluorescence extraction using polarization discrimination technique. The results indicate that, for algae water with different concentrations of IOP, the fluorescence peak will decrease while the concentration increase, but the retrieval result is still reliable when the concentration up to 300 mg·L-1. For algae water with different concentrations of chlorophyll, the concentration of chlorophyll more higher, the efficiency of extracted fluorescence using polarization method is better, for common water, this approach can still work. The study proves that the polarization method is also applicable for complex water; it is of great importance for further detecting the concentration of chlorophyll in coastal waters using remote sensing.