Olive flounder (Paralichthys olivaceus) is a key aquaculture species in South Korea, but its production has been challenged by rising mortality under environmental stress from key environmental factors such as water temperature, dissolved oxygen, and feeding conditions. To support adaptive management, this study proposes a Bayesian Deep Kernel Machine Regression (BDKMR) model that integrates Gaussian process regression with neural network-based feature learning. Using longitudinal data from commercial farms, we model fish growth as a function of water temperature, dissolved oxygen, and feed quantity. Model performance is assessed via Leave-One-Out Cross-Validation and compared against kernel ridge regression and Bayesian kernel machine regression. Results show that BDKMR achieves substantially lower prediction errors, indicating superior accuracy and robustness. These findings suggest that BDKMR offers a flexible and effective framework for predictive modeling in aquaculture systems.