Plants, by influencing water fluxes across the ecosystem-vadose zone-aquifer continuum, can leave an imprint on salt accumulation and distribution patterns. We explored how the conversion of native grasslands to oak plantations affected the abundance and distribution of salts on soils and groundwater through changes in the water balance in naturally salt-affected landscapes of Hortobagy (Hungary), a region where artificial drainage performed approximately 150 years ago lowered the water table (from -2 to -5 m) decoupling it from the surface ecosystem. Paired soil sampling and detailed soil conductivity transects revealed consistently different salt distribution patterns between grasslands and plantations, with shallow salinity losses and deep salinity gains accompanying tree establishment. Salts accumulated in the upper soil layers during pre-drainage times have remained in drained grasslands but have been flushed away under tree plantations (65 and 83% loss of chloride and sodium, respectively, in the 0 to -0.5 m depth range) as a result of a five- to 25-fold increase in infiltration rates detected under plantations. At greater depth, closer to the current water table level, the salt balance was reversed, with tree plantations gaining 2.5 kg sodium chloride m(-2) down to 6 m depth, resulting from groundwater uptake and salt exclusion by tree roots in the capillary fringe. Diurnal water table fluctuations, detected in a plantation stand but not in the neighbouring grasslands, together with salt mass balances suggest that trees consumed approximately 380 mm groundwater per year, re-establishing the discharge regime and leading to higher salt accumulation rates than those interrupted by regional drainage practices more than a century ago. The strong influences of vegetation changes on water dynamics can have cascading consequences on salt accumulation and distribution, and a broad ecohydrological perspective that explicitly considers vegetation-groundwater links is needed to anticipate and manage them.