Sea level trends and paleoclimatic conditions were studied at the ancient maritime Maya harbor of Vista Alegre and the adjacent Yalahau lagoon in the Yucatan Peninsula, Mexico. The research utilized a multi-proxy geoarchaeological approach to reconstruct the environmental geomorphological changes of the sites surroundings over the last 3,000 years. The study identified at least three significant events of relative sea-level change and coastal location shifts that impacted the shoreline morphology, directly affecting the maritime activities and settlement patterns of the ancient Maya. To characterize these environmental changes, multi-proxy earth science methods were used and integrated, including high-resolution XRF core scanning, grain-size analysis, radiocarbon dating, shallow seismic and others. The sedimentological analysis provided evidence for fluctuating climatic conditions, including periods of altered precipitation and short term high-energy marine events. These findings were correlated with the archaeological and geoarchaeological chronology of Vista Alegre to explore the interactions between the coastal environment and human adaptation. This multi-proxy study approach demonstrates that coastal archives can provide high-resolution records of environmental changes both from land and sea, offering important insights on how ancient societies navigated complex and changing maritime landscapes.