Hyperspectral technique is considered as one promising tool to solve the problems in monitoring optically-complex waters, which can be applied in optical sensors on board bouy, plane and satellite. In order to apply the technique in the in-situ chlorophyll monitoring of estuarine turbid waters, two cruises were carried out in May, 2004 and August, 2006, respectively, in Pearl River Estuary, China. In the cruises, water samples were collected at each sample station, a portable field spectroradiometer was used simultaneously to measure the downwelling sky radiance, and upwelling radiance of water and reference plaque, and the reflectance was calculated out. Further, the original reflectance spectra with 0.38 nm spectral resolution were resampled to 10 nm resolution, and then derivative spectra were processed. The results of correlation analysis between the chlorophyll-a concentrations and derivative spectra indicate that the second derivative spectra especially at 670 nm can be used to estimate chlorophyll-aconcentration of turbid estuarine waters, which suggests a new way for the in-situ chlorophyll measurement in the optically complex waters.