Abiotic factors are non-living factors such as fires and hurricanes that influence ecosystem dynamics in the estuarine ecotones. Combined with long-term climate change, fires and hurricanes will have significant impacts on the landscape. These disturbances can alter species composition and abundances either directly by removing trees and promoting species that are more resistant to perturbations, or indirectly by changing the availability of nutrients.

One way that climate change will affect the ecosystem is by altering patterns of rainfall. If rainfall is reduced, the volume of freshwater surface flow and groundwater intrusion into the estuarine ecotones will be reduced. With a shorter hydroperiod, or depth of water, the likelihood of fires may increase. Climate change also may increase the rate of sea level rise, leading to a shift in the physical location of the estuarine ecotone. Intense hurricanes too may become more common, which can lead to nutrient enrichment in the ecotones as storm surge waters carry marine phosphorus inland.

During Phase I of the FCE-LTER project, researchers began to document the long-term changes in the size and location of the estuarine ecotones in response to sea level rise, hurricanes, increased freshwater inflows, and fire. They expected that, over intermediate time scales (years to decades), the sea level rise and hurricanes will force the estuarine boundary of the ecotone landward, while increased freshwater inflows and fire will either force the freshwater boundary seaward or hold it near its current location. In the long term, though (decades to a century), scientists expected marine forces to prevail and the entire ecotone region to shift landward.