Although experiencing strong anthropogenic pressures in many estuaries, the ecology of tidal freshwater areas remains largely undocumented. As part of a restoration project in the freshwater zone of the Schelde estuary (Belgium), a new tidal habitat restoration technique (Controlled Reduced Tide system, CRT) was hypothesised to successfully compensate for the impairment of contemporary habitats. The suitability of this newly-created habitat (CRT) and the estuary was investigated over a period of three years for its macroinvertebrate community development. In both the estuary and the CRT, habitats along a flooding gradient were monitored. Differences between the CRT and reference sites in community functioning were explored according to environmental characteristics and organism biological attributes using the RLQ ordination analysis together with the fourth-corner method. Frequently flooded reference sites exhibited environmental characteristics resulting from a hydrological shear stress. In the CRT, after a rapid removal of the terrestrial fauna at low and mid elevations, the low-energy hydrology led to taxonomic and functional enrichment. The RLQ analysis produced significant environmental filtering of biological attributes mainly related to the terrestrial aquatic transition and to the environmental stressors. This provides an example of life history modification via estuarine ecosystem management.