Habitat degradation and fragmentation reduce habitat structural complexity (e.g. amount of physical features) and increase habitat edges. While many studies have focused on the effects of habitat edges or complexity on biodiversity, relatively few have disentangled them or investigated their effects over time. We investigated how proximity to the edge of eelgrass Zostera subg. Zostera marina Linnaeus, 1753 habitat, shoot density and their interactions across seasons can influence the diversity pattern of epifaunal assemblages in meadows situated in a Mediterranean lagoon (France). We used a combination of field sampling and in situ manipulations with artificial seagrass units (ASUs) mimicking low and high shoot densities. During autumn and spring, we found that shoot density, Z. marina biomass and leaf area index (LAI) were higher inside the meadows than at the edge, while epiphyte load was the highest in spring at the edges. Epifaunal abundance and diversity were higher at the edge than inside the meadow for both natural shoots—regardless of the epiphyte load—and ASUs in spring. In autumn, epifaunal abundance varied positively with ASU density, regardless of the position in the meadow. Our results also showed that edges and habitat complexity affect the epifaunal structure differently across seasons. Therefore, we suggest that recruitment of macrofauna is the main mechanism explaining a positive edge effect during spring. This work highlights the need to consider seasonal dynamics in the assessment of habitat fragmentation and degradation.