This study presents a comprehensive spatiotemporal analysis of sea surface temperatures (SST) and surface air temperatures (TAS) across 15 Mediterranean coastal stations, leveraging centennial-scale data to analyze regional climate dynamics. The modeling framework integrates three sequential phases: data preprocessing, statistical analysis, and advanced machine learning techniques, creating a robust analytical pipeline. The data preprocessing phase harmonizes diverse datasets, addresses missing values, and applies transformations to ensure analytical consistency. The statistical modeling employs the Pettitt test for change point detection and linear trend analysis to unveil underlying patterns. The machine learning phase utilizes K-means clustering for climate regime classification and implements tailored Convolutional Neural Networks (CNNs) for cluster-specific future climate anomaly projections. Results unveil a marked anthropogenic climate signal, with contemporary observations consistently surpassing historical baselines. Breakpoint analyses and linear trend assessments reveal heterogeneous climatic shifts, with pronounced warming in the northern Mediterranean. Notably, Nice and Ajaccio exhibit the highest SST increases (0.0119 and 0.0113 °C/decade, respectively), contrasting with more modest trends in Alexandria (0.0052 °C/decade) and Antalya (0.0047 °C/decade) in the eastern Mediterranean. The application of clustering and CNN projections provides granular insights into differential warming trajectories. By 2050, cooler northwestern Mediterranean zones are projected to experience dramatic SST anomalies of approximately 3 °C above the average, with corresponding TAS increases of 2.5 °C. In contrast, warmer eastern and southern regions display more subdued warming patterns, with projected SST and TAS increases of 1.5–2.5 °C by mid-century. This research’s importance is highlighted by its potential to inform tailored adaptation strategies and contribute to the theoretical understanding of climate dynamics, advancing climate modeling and analysis efforts.