The variability of the upper water hydrographic structure, the efficacy of the different schemes for estimating the mixed layer depth (MLD), the inter-comparability estimation of the MLDs and diurnal and intra-annual MLD climatology in the tropical waters in the northern South China Sea were accessed in 702 depth-profiles of potential temperature (θ) and salinity collected in 64 cruises between 17.5 and 18.5°N and 115.3 and 116.3°E from 1997 to 2013. The hydrographic structure may be sub-divided into three principal types: the classical type, with quasi-isopycnal surface mixed layer followed by an abrupt increase in the depth-gradient in θ and potential density (σθ) to mark the MLD; the stepwise type, with one or more small stepwise decreases in θ and/or increases in σθ in the mixed layer; and the graded type, with a general decrease in θ and increases in σθ with depth into the main pycnocline without a clear break to mark the MLD. These three types of upper waters were found in 75, 10, and 15% of the cruises. Out of the 10 schemes for estimating the MLD, only the fixed temperature difference method of 0.5 and 0.8°C from the 10-m temperature yielded consistent results, with root mean square error and mean absolute percentage difference of 2 m and 2%. MLD varied diurnally with an average standard deviation of 4 m from the mean. The monthly average MLD reached a maximum of 80 m in December/January and dropped to a minimum of 25 m in May.