We report hydrogeochemical and isotopic observations across the Baltic Sea from two research expeditions: (1) a ~5000 km cruise-track onboard the R/V Skagerak in 2023 and (2) a land-based sampling for terrestrial endmembers in 2024. The ship-based observations include continuous monitoring of hydrographic parameters, pH, and 222Rn in surface water. In addition, we collected 542 discrete samples from the water column, vertical profiles (n = 69 stations), and meteorological data. Land observations include discrete samples from beach groundwater (n = 77), nearshore surface water (n = 47), and rivers close to the coastline (n = 46). Discrete samples were analyzed for short-lived radium isotopes, nutrients, dissolved organic and inorganic carbon, total dissolved nitrogen, total alkalinity, methane, and stable isotopes (δ18OH2O, δ2HH2O, δ13CDIC, δ13CCO2, δ13CCH4). Data products include seven open-access files. This dataset forms the deposit for upcoming original research publications. This dataset will also be valuable to researchers interested in the hydrogeochemistry of coastal seas, like the Baltic Sea, and more generally interested in submarine groundwater discharge and estuarine biogeochemistry.