Pearl River Delta (PRD), as one of the most densely populated regions in the world, is facing both natural changes (e.g., sea level rise) and human-induced changes (e.g., dredging for navigation and land reclamation). Bathymetric information is thus important for the protection and management of the estuarine environment, but little effort has been made to comprehensively evaluate the performance of different methods and datasets. In this study, two linear regression models—the linear band model and the log-transformed band ratio model, and two non-linear regression models—the support vector regression model and the random forest regression model—were applied to Landsat 8 (L8) and Sentinel-2 (S2) imagery for bathymetry mapping in 2019 and 2020. Results suggested that a priori area clustering based on spectral features using the K-means algorithm improved estimation accuracy. The random forest regression model performed best, and the three-band combinations outperformed two-band combinations in all models. When the non-linear models were applied with three-band combination (red, green, blue) to L8 and S2 imagery, the Root Mean Square Error (Mean Absolute Error) decreased by 23.10% (35.53%), and the coefficient of determination (Kling-Gupta efficiency) increased by 0.08 (0.09) on average, compared to those using the linear regression models. Despite the differences in spatial resolution and band wavelength, L8 and S2 performed similarly in bathymetry estimation. This study quantified the relative performance of different models and may shed light on the potential combination of multiple data sources for more timely and accurate bathymetry mapping.