Shallow coastal aquifers are vulnerable hydrosystems controlled by many factors, related to climate, seawater-freshwater interactions and human activity. That is especially true for freshwater lenses situated in sandbars, which are recharged only by rainfall and snowmelt infiltration. Rising sea level poses increasing risk of salinization for such groundwater resources. IPCC report forecasts that global sea level rise will reach from 29–59 cm (RCP 2.6) to 61–110 cm (RCP 8.5) until 2100, comparing to 1986–2005. Baltic Sea region is additionally affected by glacial isostatic adjustment, which results in Fennoscandia uplift and subsidence of southern Baltic coast. Therefore, sea level is determined by an interplay between global sea level rise and land movement, which strongly depend on local factors. Main goal of our work was to forecast groundwater table level until 2100 for two sandbars, Vistula Spit and Hel Spit located in southern Baltic Sea coast (Poland). For this purpose, one-dimensional numerical models of two representative unsaturated zone profiles were developed using HYDRUS-1D, calibrated with groundwater level measurements. Weather data and sea level rise predicted for moderate and high emissions scenarios (RCP 4.5 and 8.5), were implemented to the simulations. To include possible land use change, three variants of vegetation cover (pine forest, grass, bare soil) were included. The results show the largest water table rise for 8.5 RCP scenario, 75–122 cm for Vistula Spit and 69–102 cm for Hel Spit. For 4.5 RCP the average groundwater elevation is expected to increase 54–96 cm in Vistula Spit, and 53–74 cm in Hel Spit. In that case, water table is equal or only slightly higher than the sea level, which leads to significant decrease or complete salinization of shallow aquifers, especially during low recharge periods. Presented work was funded by Water4All partnership as a part of project AQUIGROW (WATER4ALL/I/37/AQUIGROW/2024).