Seagrasses display significant intraspecific phenotypic variation, allowing sub-populations to inhabit to diverse environmental conditions. Phenotypic variation between sub-populations may indicate fixed-traits to meadow-specific conditions, or environmentally induced plasticity influencing adaptability and responses to changing conditions. Understanding the drivers behind phenotypic diversity is crucial for identifying populations that are either pre-adapted to anticipated future conditions, or demonstrate a high degree of plasticity, facilitating effective acclimation to changing environments. We observed intraspecific morphological variations in four genetically distinct Zostera muelleri sub-populations, potentially associated with specific meadow environments. To determine whether observed variations, especially in response to light availability, stem from fixed traits or plasticity, a three-month mesocosm experiment duplicated over two seasons was conducted. While all populations exhibited high survival rates, one population displayed greater physiological plasticity across light treatments. Our findings underscore the importance of investigating the drivers of sub-population phenotypic variation to identify resilient donor populations better suited to withstand environmental fluctuations, thereby enhancing the long-term resilience and persistence of restored meadows.