Satellite remote sensing technology has proven effective in monitoring various environmental parameters, but its efficiency in assessing shallow lakes has been limited. This study applies state-of-the-art machine and deep learning algorithms supported by classical statistic methods to analyze remote sensing data to measure chlorophyll-a (Chl-a) concentration levels. Focused on a shallow coastal lagoon, Mar Menor, this work analyzes statistically daily Sentinel 3 information behaviour and compares Machine Learning and Deep Learning techniques to enhance efficiency and accuracy data of this satellite. Convolutional Neural Networks (CNNs) stand out as a robust choice, capable of delivering excellent results even in the presence of anomalous events. Our findings demonstrate that the CNN-based approach directly utilizing satellite data yields promising results in monitoring shallow lakes, offering enhanced efficiency and robustness. This research contributes to optimizing remote sensing data to and produce a continuous information flow addressed to monitoring shallow aquatic ecosystems with potential environmental management and conservation applications.