<p>Human-driven fragmentation of natural habitats increasingly threatens biodiversity, particularly in coastal ecosystems like seagrass meadows. Fragmentation breaks continuous habitats into smaller, isolated patches, amplifying edge effects and disrupting community structures and ecosystem functions. This study examines the effects of habitat fragmentation on large (&gt; 1 mm) and small (0.2–1 mm) epifauna, as well as infauna, within eelgrass (<i>Zostera marina</i>) meadows along the Skagerrak coast in western Sweden. We assessed faunal responses across three fragmentation levels (low, medium, and high) and patch zones (Edge, Near-Edge and Center), providing a novel multi-assemblage analysis of these dynamics. Field surveys and statistical modeling revealed distinct community responses: large epifauna, especially amphipods, dominated low and moderately fragmented meadows, whereas highly fragmented areas showed more even species distributions. In contrast, small epifauna exhibited consistent abundance across zones and fragmentation levels. Infaunal communities varied most, with high fragmentation linked to increased evenness and shifts in species composition. These findings underscore the importance of conserving less fragmented meadows and highlight the need for targeted restoration efforts to enhance biodiversity and ecological resilience in degraded areas. By addressing both patch- and seascape-level fragmentation effects, this study offers critical insights into the ecological impacts of habitat fragmentation, supporting the development of targeted conservation strategies for coastal ecosystems.</p>