The successful establishment of mangrove ecosystems depends on an intricate network of interactions among physical and biological factors that are highly dynamic through time. At millennial to centennial time scales, regional climates, sea levels, and local geomorphology play critical roles in the establishment of mangroves. Whereas fluvio-marine dynamics define coastal sedimentary settings, regional precipitation and freshwater input modulate salinity and seasonal flooding patterns. We analyzed a ~7800-year-old, continuous sedimentary record from the western coast of the Gulf of Mexico to shed light on regional biophysical coastal processes and the history of the mangroves that occupy the region today. We used a systematic sampling of mud-water interface sediments to generate a modern reference frame for interpreting fossil pollen assemblages. Our results indicate that the cored location that is currently approximately at sea level, was below sea level from ~7800 to 4000 calibrated years before present (cal BP). The establishment of dense mangrove stands took place around 3700 cal BP, when regional sea levels stabilized, resulting in a substantial increase of organic matter and therefore carbon stored in the sediments. However, the mangrove ecological succession that started at ~6000 cal BP was interrupted by a regional drought that extended from ~5400 to 3700 cal BP. From 3700 cal BP to Present, the lagoon has been characterized by relatively stable both substratum and sea level, that together have facilitated the establishment of mangrove forests. Overall, our record demonstrates the complexity of the interactions between local and regional factors in the development and evolution of both coastal geomorphology and ecosystems.