Site‐specific paleoenvironmental reconstructions are necessary to isolate environmental factors from social forces that influence shifting human practices in the coastal environment. This interdisciplinary study included the collection and analysis of marine and freshwater pond sediment cores and terrestrial sediment samples along with archaeological excavations at three directly associated pre‐Columbian sites in Horseshoe Cove on the northern Gulf Coast of Florida. This research shows a strong correlation between environmental change, the timing of initial occupation, and the morphological characteristics chosen for settlement by the pre‐Columbian residents of this area. Specific attributes sought for new settlements included elevated landforms in protected areas away from the immediate shoreline, access to fresh water from nearby spring‐fed ponds or tidal creeks, and easy access to marine resources via tidal creeks. The result of this study can be useful as a model for locating and identifying archaeological sites in similar environmental settings.