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Vertical variability in the bio-optical properties of seawater in the north South China Sea (NSCS) including inherent optical properties (IOPs) and chlorophyll a concentration (Chl) were studied on the basis of in situ data collected in summer 2008 using an absorption/attenuation spectrophotometer. An empirical model was developed to estimate Chl profiles based on the absorption line height at long wavelengths, with a relative root mean square error of 37.03％. Bio-optical properties exhibited large horizontal and vertical spatial variability. As influenced by coastal upwelling and the Zhujiang River (Pearl River) discharge, both IOPs and Chl exhibited high values in the surface waters of the inner shelf, which tended to decrease with distance offshore. Subsurface maximum layers of IOPs and Chl were observed in the middle and outer shelf regions, along with significantly higher values of attenuation coefficients beneath this layer that rapidly increased towards the bottom. In the open ocean, both IOPs and Chl exhibited consistent variability, with the subsurface maximum layer typically located at 34-84 m. Phytoplankton were found to be one of the major components in determining the vertical variability of bio-optical properties, with their vertical dynamics influenced by both physical forcing and light attenuation effects. The depth of the subsurface maximum layer was found to be closely related to the fluctuation of the oceanic thermocline and the depth of the euphotic zone, which also affected the total integrated biomass of the upper ocean. Typically high values of attenuation coefficients observed in the bottom waters of the continental shelf reflected the transport of particulate matter over the bottom boundary layer. Our results reveal large spatial differences in bio-optical profiles in response to complex marine ecodynamics in the NSCS. From the perspective of marine research, high-resolution optical measurements are clearly advantageous over conventional bottle sampling.