Climate warming due to the enhanced greenhouse effect is expected to have a significant impact on natural environment and human activity in high latitudes. Mostly, it should have a positive effect on human activity. The main threats in Estonia that could be connected with sea-level rise are the flooding of coastal areas, erosion of sandy beaches and the destruction of harbour constructions. Possible climate change and its negative impacts in the coastal regions of Estonia are estimated in this paper. Climate change scenarios for Estonia were generated using a Model for the Assessment of Greenhouse-gas Induced Climate Change (MAGICC) and a regional climate change database—SCENanario GENerator (SCENGEN). Three alternative emission scenarios were combined with data from 14 general circulation model experiments. Climate change scenarios for the year 2100 indicate a significant increase in air temperature (by 2.3–4.5 °C) and precipitation (by 5–30%) in Estonia. The highest increase is expected to take place during winter and the lowest increase in summer. Due to a long coastline (3794 km) and extensive low-lying coastal areas, global climate change through sea-level rise will strongly affect the territory of Estonia. A number of valuable natural ecosystems will be in danger. These include both marine and terrestrial systems containing rare plant communities and suitable breeding places for birds. Most sandy beaches high in recreational value will disappear. However, isostatic land uplift and the location of coastal settlements at a distance from the present coastline reduce the rate of risk. Seven case study areas characterising all the shore types of Estonia have been selected for sea-level rise vulnerability and adaptation assessment. Results and estimates of vulnerability to 1.0-m sea-level rise by 2100 are presented in this paper. This is the maximum scenario according to which the actually estimated relative sea-level rise would vary from 0.9 m (SW Estonia) to 0.7 m on the north-western coast due to different velocities of land uplift in the studied areas. The longest coastline section recession (6.4 km) would occur on the western coast of the mainland where extensive areas of reed bed and flooded meadows would relocate landwards or disappear. Possible damages in Tallinn, the capital city, would be the greatest compared to the other study areas. The greatest threat to the environment of the Gulf of Finland and the whole Baltic Sea is the dumping site of the former uranium enrichment plant in Sillamäe which is situated very close to the coastline and can be easily influenced during storms.