Sea-level rise demands for protection measures of endangered coastlines crucial for the local population. At the island of Sylt in the SE North Sea, shoreline erosion is compensated by replenishment with sand dredged from an offshore extraction site. We studied the long-term effects of sand extraction on bathymetry, geomorphology, habitats and benthic fauna. Sand extraction created dredging holes about 1 km in diameter and up to 20 m below the ambient seafloor level. Directly after dredging the superficial sediment layer, inside the pits was dominated by coarse sand and stones. Hydroacoustic surveys revealed only minor changes of bathymetry > 35 years after sand extraction. Obviously, backfill of the dredging pits was very slow, at a rate of a few millimeters per year, presumably resulting from low ambient sediment availability and relatively calm hydrodynamic conditions despite high wave energy during storms. Thus, a complete backfill of the deep extraction sites is likely to take centuries in this area. Hydroacoustic surveys and ground truthing showed that the backfilled material is mainly very fine sand and mud, turning the previously coarse sand surface into a muddy habitat. Accordingly, grab samples revealed significant differences in macrozoobenthos community composition, abundance and species density between recently dredged areas (< 10 years ago), recovery sites (dredging activity > 10 years ago) and undisturbed sites (control sites). Overall, dredging turned the original association of sand-dwelling species into a muddy sediment association. Since re-establishment of disturbed benthic communities depends on previous re-establishment of habitat characteristics, the low sedimentation rates indicate that a return to a pre-dredging habitat type with its former benthic community and habitat characteristics is unlikely. Since coarse sand is virtually immobile in this area, a regeneration towards pre-dredging conditions is also unlikely without human interference (e.g., mitigation measures like depositing coarse material on the seafloor to restore the sessile epifauna).