Bathymetry data is indispensable for a variety of aquatic field studies and benthic resource inventories. Determining water depth can be accomplished through an echo sounding system or remote estimation utilizing space-borne and air-borne data across diverse environments, such as lakes, rivers, seas, or lagoons. Despite being a common option for bathymetry mapping, the use of satellite imagery faces challenges due to the complex inherent optical properties of water bodies (e.g., turbid water), satellite spatial resolution limitations, and constraints in the performance of retrieval models. This study focuses on advancing the remote sensing based method by harnessing the non-linear learning capabilities of the machine learning (ML) model, employing advanced feature selection through a meta-heuristic algorithm, and using image extraction techniques (i.e., band ratio, gray scale morphological operation, and morphological multi-scale decomposition). Herein, we validate the predictive capabilities of six ML models: Random Forest (RF), Support Vector Machine (SVM), CatBoost (CB), Extreme Gradient Boost (XGB), Light Gradient Boosting Machine (LGBM), and KTBoost (KTB) models, both with and without the application of meta-heuristic optimization (i.e., Dragon Fly, Particle Swarm Optimization, and Grey Wolf Optimization), to accurately ascertain water depth. This is achieved using a diverse input dataset derived from multi-spectral Landsat 9 imagery captured on a cloud-free day (19 September 2023) in a shallow, turbid lagoon. Our findings indicate the superior performance of LGBM coupled with Particle Swamp Optimization (R2 = 0.908, RMSE = 0.31 m), affirming the consistency and reliability of the feature extraction and selection-based framework, while offering novel insights into the expansion of bathymetric mapping in complex aquatic environments.