Rising sea level represents a significant threat to coastal communities and ecosystems, including altered habitats and increased vulnerability to coastal storms and recurrent inundation. This threat is exemplified in the northern Gulf of Mexico, where low topography, marshes, and a prevalence of tropical storms have resulted in extensive coastal impacts. The ability to facilitate adaptation and mitigation measures relies, in part, on the development of robust predictive capabilities that incorporate complex biological processes with physical dynamics. Initiated in 2010, the 6-year Ecological Effects of Sea Level Rise—Northern Gulf of Mexico project applied a transdisciplinary science approach to develop a suite of integrated modeling platforms informed by empirical data that are capable of evaluating a range of climate change scenarios. This special issue highlights resultant integrated models focused on tidal hydrodynamics, shoreline morphology, oyster ecology, coastal wetland vulnerability, and storm surges that demonstrate the need for dynamic models to incorporate feedbacks among physical and biological processes in assessments of sea level rise effects on coastal systems. Effects are projected to be significant, spatially variable and nonlinear relative to sea level rise rates. Scenarios of higher sea level rise rates are projected to exceed thresholds of wetland sustainability, and many regions will experience enhanced storm surges. Influenced by an extensive collaborative stakeholder engagement process, these assessments on the coastal dynamics of sea level rise provide a strong foundation for resilience measures in the northern Gulf of Mexico and a transferable approach for application to other coastal regions throughout the world.