An in situ field high-frequency bio-optical measurement was carried out in the littoral region in Meiliang Bay of Lake Taihu, a large shallow lake of China from 24 July to 1 August in 2010. The underwater irradiance, beam attenuation coefficient and absorption coefficient, the related physical-chemical and meteorological parameters were measured and analyzed, in order to determine the relationship between water bio-optical properties and wind waves process. The absorption coefficients of particles a(p) (440), non-phytoplankton a(d) (440), phytoplankton a(ph) (440) and chromophoric dissolved organic matter (CDOM) a(CDOM) (440) were 3.97, 3.97, 6.58 m(-1); 1.69, 2.17, 4.20 m(-1); 2.28, 1.80, 1.33 m(-1); 1.05, 1.04, 1.08 m(-1) with the corresponding 30-minute average wind speed of <3, 3-5 and >5 m x s(-1) under small, middle and large wind and waves, respectively. Phytoplankton particles contributed the most to total absorption coefficient integrated over a range of photosynthetically active radiation (PAR) (400-700 nm) with a value of 42.5% during small wind waves. With the increase of wind speed, the relative contributions of phytoplankton, CDOM and pure water deceased but the relative contribution of non-phytoplankton significantly increased with the values of 33.0%, 41.7% and 52.0% during small, middle and large wind waves, respectively. A significantly positive linear relationship was found between PAR diffuse attenuation coefficients and the mean wind speed within 10 minutes. Sediment resuspension caused by wind waves had a significant effect on PAR diffuse attenuation coefficient. From small wind waves to large wind waves, PAR diffuse attenuation increased 80.0% but the euphotic depth decreased 42.2%. Significant linear relationships were found between PAR diffuse attenuation coefficient, the beam attenuation coefficients at 750 nm, total suspended solid concentration and wind speed, wave height, wave shear stress, in which the correlation between PAR attenuation coefficients and meteorological hydrology factors was most significant. High-frequency bio-optical measurement showed that hydrodynamic process significantly affected the short-term variation of bio-optical properties in algal-dominated lake region of shallow lake through sediment resuspension, mixing and migration of phytoplankton.