It was found that water temperature is the key environmental variable correlated with fish kills and sea turtle cold stunning, hence the challenge to accurately predict future water temperatures with long lead times. Artificial neural network models were trained and tested over past hourly measurements of water and air temperatures in the Laguna and the nearby coastline of the much larger Gulf of Mexico. The optimization process, the predictors and the neural network topologies selected for the different lead times will be described. The performance was assessed for varying prediction times (3, 12, 24, 48 and up to 84 hours). To assess model performance more specifically during cold events, performance metrics were also assessed during times for target water temperature below 12°C. Results confirm the applicability of the models for cold events. While shallow neural networks are implemented operationally, additional research is ongoing to compare performance of shallow neural networks with deep neural networks applied to the same data. Given the large number of inputs selected for the operational models (over 100 predictors) and the large data sets (over 3 million data points per time series) a deep learning approach was deemed promising. The deep learning technique selected is the stacked denoising autoencoder (SDAE) whereby hidden layers are pretrained in an unsupervised manner in order to create a higher order representation of the features. The optimal SDAE architecture will be described along with a comparison of the results of the two types machine learning approaches, shallow and deep neural networks.