Restoration engineering measures, such as managed realignments or building groins, modify the environmental characteristics of coastal intertidal ecosystems. Creating physical modifications that are beneficial to an intertidal system's ecology necessitates an in-depth understanding of the relationships between the abiotic and biotic components of a given intertidal habitat. In this study, we evaluate how hydrodynamics and sediment characteristics drive the development of the benthic macrofauna community during the first 5 years following engineering measures to enhance benthic macrofauna diversity at three locations. The creation of low-energy habitats through groins (Knuitershoek and Baalhoek) and a managed realignment dike breach (Perkpolder) led to the accumulation of fine sediments in all three impact sites. Biomass of benthic macrofauna quickly increased between 2016 and 2020, with successional processes being more important in Perkpolder, where the habitat was started completely from scratch due to a managed realignment, than at Knuitershoek or Baalhoek, where habitat conditions were improved by adding groins. In addition, the density of benthos-eating birds, especially oystercatchers, increased at some of the modified sites. While a low-energy habitat may harbor more diverse assemblages of benthic macrofauna than a highly dynamic one, the extremely high silt content, which is typical for low-energy habitats, may slow benthic community development. The observed increase of biomass at our impact sites highlights the value of the interventions, while the delays in the response of the benthic macrofauna community emphasizes the need for extensive monitoring both in time and space and the identification of underlying abiotic–biotic mechanisms.