A regional climate model (RCM) and oceanographic, hydrological and digital elevation models were applied to study the impact of climate change on surface wind, sea level, river discharge, and flood prone areas in the Baltic Sea region. The RCM was driven by two global models and two emission scenarios. According to the four investigated regional scenario simulations, wind speed in winter is projected to increase between 3 and 19% as an area average over the Baltic Sea. Although extremes of the wind speed will increase about as much as the mean wind speed, sea level extremes will increase more than the mean sea level, especially along the eastern Baltic coasts. In these areas projected storm events and global average sea level rise may cause an increased risk for flooding. However, the Swedish east coast will be less affected because mainly the west wind component in winter would increase and because land uplift would compensate for increased sea levels, at least in the northern parts of the Baltic. One of the aims of the downscaling approach was to investigate the future risk of flooding in the Lake Mälaren region including Stockholm city. In Stockholm the 100-year surge is projected to change between -51 and 53 cm relative to present mean sea level suggesting that in the city the risk of flooding from the Baltic Sea is relatively small because the critical height of the jetty walls will not be exceeded. Lake Mälaren lies just to the west of Stockholm and flows directly into the Baltic Sea to the east. This study addresses also the question of how the water level in Lake Mälaren may be affected by climate change by incorporating the following three contributing components into an analysis: 1) projected changes to hydrological inflows to Lake Mälaren, 2) changes to downstream water levels in the Baltic Sea, and 3) changes in outflow regulation from the lake. The first component is analyzed using hydrological modeling. The second and third components employ the use of a lake discharge model. An important conclusion is that projected changes to hydrological inflows show a stronger impact on lake levels than projected changes in water level for the Baltic Sea. Furthermore, an identified need for increased outflow capacity from the lake for the present climate does not diminish with projections of future climate change. The tools developed in this work provide valuable inputs to planning for both present and future operations of water level in Lake Mälaren. Based on the oceanographic and hydrological scenario simulations, flood prone areas were analysed in detail for two municipalities, namely Ekerö and Stockholm. The GIS analysis of both municipalities indicates a series of affected areas. However, in case of the 100-year flood (0.65 m above the mean lake level) in present climate or even in case of the maximum probable flood (1.48 m above the mean lake level) the potential risks will be relatively low.