For the large-scale coastal wetland system of the Baltic Sea, this study develops a methodology for investigating if and to what degree the variability and changes in certain hydro-climatic drivers control key coastal-marine physical conditions. The studied physical conditions include: (a) water temperature, (b) water salinity, and (c) flow structures (magnitudes and directions of flows between marine basins and the associated coastal zones and wetlands). We use numerical simulations of three hydro-climatically distinct cases to investigate the variations in hydro-climatic drivers and the resulting physical conditions (a-c) among the cases. The studied hydro-climatic forcing variables are: net surface heat flux, wind conditions, saltwater influx from the North Sea, and freshwater runoff from land. For these variables, the available observation-based data show that the total runoff from land is significantly and positively correlated with precipitation on the sea itself, and negatively correlated with saltwater influx from the North Sea to the Baltic Sea. Overall, the physical condition (a-c) variability in the Baltic Sea and its coastal zones is found to be pairwise well-explained by simulation case differences as follows: (a) Net heat flux is a main control of sea water temperature. (b) Runoff from land, along with the correlated salt water influx from the North Sea, controls average sea salinity; with the variability of local river discharges shifting some coastal zones to deviate from the average sea condition. (c) Wind variability and change control the Baltic Sea flow structure, primarily in terms of flow magnitude and less so in terms of flow direction. For specific coastal wetland zones, considerable salinity differences from average Baltic Sea conditions (due to variability in local river discharges) are found for the coasts of Finland and Estonia, while the coastal wetland zones of south-eastern Sweden, and of Estonia and Latvia, emerge as particularly sensitive to wind shifts.