Artificial substrates are omnipresent today in most estuaries mostly in form of massive rip-rap used for groynes and jetties. In the Weser estuary, Germany, 60% of the shoreline is covered with such artificial substrates while, natural rocky substrate is lacking, as in all Wadden Sea estuaries. This large quantity of artificial substrates may be colonized by a benthic hard-substrate community which differs from the local natural soft-substrate assemblage. In this study we examined species compositions, abundances, biomass, and numbers of species of subtidal benthic communities on groynes and in the natural habitat, the sediment, along the salinity gradient of the Weser estuary. Species composition changed on both substrates significantly with salinity and was also significantly different between the substrates. In a comparison with the sediment, the groynes did not provide any benefit for non-indigenous nor for endangered species in terms of abundance, biomass, and number of species, but represent habitats with higher total abundances and biomass; though some non-indigenous species even occurred exclusively on groynes. In particular, groynes supported filter-feeding organisms which play an important role by linking benthic and pelagic food webs. The dominance of the suspension feeders affects crucial estuarine ecosystem services and may have important implications for the estuarine management by altering the estuarine ecological quality status. Hence, artificial substrates should be considered in future conservation planning and in ecological quality monitoring of the benthic fauna according to the European Water Framework Directive.