Abstract. We analyse the cumulative impacts of climate change in a complex basin-lagoon-sea system continuum, which covers the Nemunas River basin, Curonian Lagoon, and the south-eastern part of the Baltic Sea. A unique state-of-the-art coupled modelling system, consisting of hydrological and hydrodynamic models, has been developed and used for this purpose. Results of four regional downscaled models from the Rossby Centre high-resolution regional atmospheric climate model have been bias-corrected using in situ measurements, and were used as forcing to assess the changes that the continuum will undergo until the end of this century. Results show that the Curonian Lagoon will be subjected to higher river discharges that in turn increase the outgoing fluxes into the Baltic Sea. Through these higher fluxes, both the water residence time and saltwater intrusion event frequency will decrease. Most of these changes will be more pronounced in the northern part of the lagoon, which is more likely to be influenced by the variations in the Nemunas River discharge. The southern part of the lagoon will experience lesser changes. Water temperatures in the entire lagoon and the south-eastern Baltic Sea will steadily increase, and salinity values will decrease. However, the foreseen changes in physical characteristics are not of the scale suggesting significant shifts in the ecosystem functioning, but are expected to manifest in some quantitative alterations in the nutrient retention capacity. However, some ecosystem services such as ice fishing are expected to vanish completely due to the loss of ice cover.