Traditionally, temperature-salinity (T-S) relationship was analysed to indicate the characteristic of water mass, and prediction models based on regression may be built to estimate the salinity in earlier researches. Temperature-salinity characteristic however might change dynamically with respect to the geographic location, season, or water layer, and is quite sensitive to the depth for the same location. It is therefore of interest whether including depth into the regression model could help to improve the prediction accuracy. In this paper, multivariate nonlinear regression is investigated to predict the salinity according to both temperature and depth. Experimental results show that depth is very effective for improving the prediction accuracy, and season-dependent model may achieve better performance than season-independent model. In addition, when the analysis was conducted for 5-year range, it is found the prediction accuracy is significantly higher than the result for all years, which indicates there might exist long-term variation on the characteristics of the water masses. Furthermore, 3D model and visualization scheme were proposed to explore the effect of depth on the temperature-salinity-depth characteristic, and a visualization system was built accordingly. This system may present the T-S curve and 3D Model according to the assigned criteria of season or multi-year range, and allows the user to view the similarity map for the given T-S-D data so as to conduct comparative study of water masses for a wide area of ocean.