Seagrass meadows ecosystem engineering effects are correlated to their density (which is in turn linked to seasonal cycles) and often cannot be perceived below a given threshold level of engineer density. The density and biomass of seagrass meadows (Z. marina) together with associated macrophytes undergo substantial seasonal changes, with clear declines in winter. The present study aims to test whether the seasonal changes in the density of recovering seagrass meadows affect the benthic food webs of the southern Baltic Sea (Puck Bay). It includes meiofauna, macrofauna and fish of vegetated and unvegetated habitats in summer and winter seasons. Two levels of organization have been tested – species-specific diet preferences using stable isotopes (δ13C, δ15N) in Bayesian mixing models (MixSIAR) and the community-scale food web characteristics by means of isotopic niches (SIBER). Between-habitat differences were observed for grazers, as a greater food source diversity in species from vegetated habitats was noted in both seasons. Larger between-habitat differences in winter were documented for suspension/detritus feeders. The community-wide approach showed that the differences between the habitats were greater in winter than in summer (as indicated by the lower overlap of the respective isotope niches). Overall, the presence of seagrass meadows increased ecological stability (in terms of the range of food sources utilized by consumers) in the faunal assemblage, while invertebrates from unvegetated areas shifted their diet to cope with winter conditions. Therefore, as a more complex system, not sensitive to seasonal changes, Z. marina meadows create a stable habitat with high resilience potential.