The Slikken van Flakkee, a former tidal wetland in the Grevelingen, the Netherlands, has been changing under freshening conditions since 1971; in that year, the salty Grevelingen estuary was closed from the North Sea as part of the Dutch Delta Works. Our research aimed to analyse vegetation development over 1972–2016 and relates succession to quantified ecohydrogeochemical processes in the Slikken van Flakkee. We analysed succession and physico-chemical conditions at 63 monitoring locations. Based on extensive fieldwork in 2016 and 2017, we quantified the identified geochemical processes via inverse modelling and applied Canonical Correspondence Analysis (CCA) to search for interrelations with vegetation. Nine per cent of the 229 observed plant species are rare and threatened or vulnerable, according to the Dutch Red List. Succession series showed a development from saline pioneer communities towards grassland and shrub vegetation dependent on management measures (grazing and mowing versus spontaneous development), desalinisation and geochemical processes, of which dissolution of carbonates appeared to be the dominant one. During desalinisation, the water-type shifted from NaCl towards CaHCO3. The CCA confirmed the impact of geochemical and texture variables, elevation and management on vegetation. Grazing and mowing led to species-rich grasslands and forb vegetation harbouring twice as many species than the spontaneously developed area after 50 years, demonstrating the importance of active nature management. We argue that hydrological-geochemical modelling is necessary to support policy-making before deciding on the partial re-establishment of the tide in Lake Grevelingen.