Seagrass ecosystems play a vital role in marine environments, providing essential services, and supporting a diversity of fauna and algae that are critical components in marine trophic structures. However, global and local seagrass declines due to various influences raise concerns about the health of these ecosystems. This study investigated the structural and environmental drivers influencing epifaunal communities associated with the dwarf eelgrass ( Zostera capensis), in a temperate lagoon ecosystem. Variation in epifaunal patterns across phenotypically distinct seagrass populations were observed. Large-leaved morphotypes in deeper intertidal stands near the lagoon mouth exhibited higher species diversity and richness. Conversely, small-leaved populations in higher shore stands supported greater species abundances, notably, two desiccation-resistant gastropods, Assiminea sp. and Siphonaria compressa. Seasonal differences in epifauna were significant, with higher abundances observed during spring and summer, while diversity and richness peaked in autumn and winter. Several key factors influencing epifaunal abundances were identified. The results of structural equation modelling showed seagrass shoot densities and leaf width to have positive direct effects, with light (turbidity) and oxygen levels also playing important roles. Temperature, pH, and exposure indirectly affected epifaunal abundances, however, temperature had a direct effect on seagrass structure and significantly influenced five out of six seagrass metrics measured. Ongoing assessments of seagrass distribution in the lagoon indicate more significant declines in populations near to the lagoon mouth, suggesting a simultaneous reduction in associated epifaunal communities reliant on large-leaved seagrass beds. As climate change-induced warming continues, further declines in seagrass populations are anticipated, particularly in large-leaved varieties. This trend is likely to have adverse consequences for the associated epifaunal communities and other trophic levels within the ecosystem. Given the significance of seagrass habitats for food provision and sustaining livelihoods, the loss of these ecosystems could have far-reaching consequences. Preserving seagrass ecosystems is therefore crucial to ensuring the continued provision of these ecosystem services.