In this study, vertical profiles of velocity and hydrographic properties measured by the Lowered ADCP and CTD, respectively are used to calculate the vertical eddy diffusivity K based on small-scale turbulence theory. Two methods are used to estimate K, that is, the Thorpe scale analysis method (designated as Kz) and vertical wave number shear spectral method (designated as Ksh). Four different experiments with different flow conditions and bathymetry, i.e., internal tides, deep open-ocean, nonlinear internal waves and Kuroshio, are conducted and their K values are estimated and discussed. The internal tides at the mouth of Kao-Ping Submarine Canyon (KPSC) are observed during July and December (spring tide) of 2008. In each cruise the LADCP/CTD casts are repeated every two hours and last 27 and 40 hours, respectively. The results indicate the existence of strong, semi-diurnal internal tides with vertical displacement of 50~100 m and the nature of first baroclinic mode. Turbulent mixing during flood is significantly stronger than that during ebb. Note that in the winter experiments the Kz can reach 0.01 m2 s-1, which is even larger than the reported Kz values in other submarine canyons of the world, suggesting strong mixing processes are taking place in the KPSC. From the LADCP/CTD data of the joint hydrographic survey on May 2008 at SEATS station of the South China Sea, the estimated average values of Kz and Ksh in the upper 3000 m are about 3¡Ñ10-4 m2 s-1 and 1.8¡Ñ10-4 m2 s-1, respectively. The average value of Kz near the ocean bottom increases to 2.5¡Ñ10-3 m2 s-1. These estimated Kz are somewhat larger than the reported values in the open ocean. On the other hand, Kz values between 300 and 700 m deep are almost zero, indicating that turbulent mixing is inhibited in the stratified layer. Nonlinear internal waves are tracked in the South China Sea during May 2007. Our results show that after the internal solitons passed in the deep waters, the Kz profiles change significantly, surface mixing is weak, and Kz increases gradually from 400 m deep to the ocean bottom. In the shallow water region, shoaling effect of the nonlinear internal waves lead to enhanced energy dissipation and higher values of Kz, with the maximum value reaches 1 m2 s-1 near 180m depth. The flow structure of Kuroshio current between Taiwan and Lanyu is observed in October 2007. The results show that Kz in the surface layer is high (~10-2 m2 s-1), obviously due to strong Kuroshio flows there. At the 3000 m deep submarine trench near Lanyu, the Kz in the bottom layer is also very high (~ 1 m2 s-1 ), indicating that effective turbulent mixing in the bottom layer is mainly due to topography, which has similar level as the nonlinear internal waves.