This study delves into the intricate dynamics between wave activity and marine vegetation, focusing on <em>Posidonia oceanica</em> meadows in the Mediterranean Sea along the Civitavecchia coastal zone (north-eastern Tyrrhenian Sea, Italy). Traditional modeling approaches often oversimplify wave-vegetation interactions and overlook the necessity for robust in-situ observational systems, which can lead to inadequate representations of the dynamic environments where seagrasses thrive. The Digital Twin modelling framework presents a compelling solution, offering comprehensive insights that enhance decision-making for coastal management. We advance wave-vegetation modeling by integrating a refined seagrass representation that encompasses flexibility, seasonal growth dynamics, and phenotypic traits, all informed by site-specific measurements. Applying this model to the Civitavecchia coast demonstrated that integrating observed seasonal variability into the numerical model was crucial for obtaining realistic results. This revealed a mean monthly wave damping capacity variation of up to 10 %, intricately driven by seasonal growth dynamics. Spatial assessments unveiled wave height reductions ranging from 10 % to 40 %, with an average attenuation of 18 % across Sites of Community Importance and 24 % for seagrass traits over rocky substrate. These findings offer valuable insights into the role of seagrasses as nature-based solution, facilitating more effective coastal management strategies and guiding restoration efforts in vulnerable marine ecosystems.