Fluorescence excitation-emission matrix spectroscopy (EEMs) combined with absorption spectroscopy were applied to study the optical properties of CDOM samples from highly-polluted Yundang Lagoon in Xiamen in order to demonstrate the feasibility of using these spectral properties as a tracer of the degree of organic pollution in similar polluted coastal waters. Surface water samples were collected from 13 stations 4 times during April and May, 2008. Parallel factor analysis (PARAFAC) model was used to resolve the EEMs of CDOM. Five separate fluorescent components were identified, including two humic-like components (C1: 240, 325/422 nm; C5: 260, 380/474 nm), two protein-like components (C2: 225, 275/350 nm; C4: 240, 300/354 nm) and one xenobiotic-like component (C3: 225/342 nm), which could be used as a good tracer for the input of the anthropogenic organic pollutants. The concentrations of component C3 and dissolved organic carbon (DOC) are much higher near the inlet of sewage discharge, demonstrating that the discharge of surrounding sewage is a major source of organic pollutants in Yundang Lagoon. CDOM absorption coefficient a(280) and the score of humic-like component C1 showed significant linear relationships with CODMn, and a strong positive correlation was also found between the score of protein-like component C2 and BOD5. This suggested that the optical properties of CDOM may provide a fast in-situ way to monitor the variation of the water quality in Yundang Lagoon and that of similar polluted coastal waters.