Coastal risk reduction features are often built to protect infrastructure and ecosystems from damaging waves, sea level rise, and shoreline erosion. Engineers often use predictive numerical modeling tools, such as Delft3D to help design optimal intervention strategies. Still, their use by coastal managers for optimizing the design of living shorelines in complex geomorphic environments has been limited. In this study, the Delft3D modeling suite is used to help select the optimum living shoreline structure for a complex inlet and bay system at Carancahua Bay, Texas. To achieve this goal, an extensive array of sensors was deployed to collect hydrodynamic and geotechnical data in the field, and historical shoreline changes were assessed using image analysis. The measured data were then used to parameterize and validate the baseline Delft3D model. Using this validated model, the hydrodynamics resulting from a series of structural alternatives were simulated and compared. The results showed that the mouth of this complex inlet has widened greatly since the 1800s due to wave erosion and sea level rise. The analysis of the structural alternatives showed it was not advisable to attempt a return of the inlet to its historical extent, but rather to create a hybrid design that allowed for limited flow to continue through a secondary inlet. The numerical modeling effort helped to identify how to best reduce wave and flow energy. This study provides a template for the application of Delft3D as a tool for living shoreline design selection under complex shallow-estuary and inlet dynamics.