Retrieving the water depth by satellite is a rapid and effective method for obtaining underwater terrain. In the optical shallow waters, the bottom signal has a great impact on the radiation from the water which related to water depth. In the optical shallow waters, the spatial distribution characteristic of water quality parameters derived by the updated quasi analysis algorithm (UQAA) is highly correlated with the bottom brightness. Because the bottom reflection signal is strongly correlated with the spatial distribution of water depth, the derived water quality parameters may helpful and applicable for optical remote sensing based satellite derived bathymetry. Therefore, the influence on bathymetry retrieval of the UQAA IOPs is worth discussing. In this article, different machine learning algorithms using a UQAA were tested and remote sensing reflectance at water depth in situ points and their detection accuracy were evaluated by using Worldwiew-2 multispectral remote sensing images and laser measurement data. A backpropagation (BP) neural network, extreme value learning machine (ELM), random forest (RF), Adaboost, and support vector regression (SVR) machine models were utilized to compute the water depth retrieval of Ganquan Island in the South China Sea. According to the obtained results, bathymetry using the UQAA and remote sensing reflectance is better than that computed using only remote sensing reflectance, in which the overall improvements in the root mean square error (RMSE) were 1 cm to 5 cm and the overall improvement in the mean relative error (MRE) was 1% to 5%. The results showed that the results of the UQAA could be used as a main water depth estimation eigenvalue to increase water depth estimation accuracy.