This work presents monthly budgets for water and salt in the Baltic Sea and its five main subbasins, the Baltic Proper, the Bothnian Sea, the Bothnian Bay, the Gulf of Finland, and the Gulf of Riga. This process-based mass-balance model uses empirical data (from Helsinki Commission [HELCOM]) for the period 1997 to 2005. Previous models of this kind generally have used water-temperature data to differentiate between different water layers. This model (CoastMab) uses sedimentological criteria related to the theoretical wave base to differentiate between the surface-water layer and lower vertical layers. CoastMab stems from a model development in aquatic radioecology, and it has been previously validated for many different substances (radionuclides, metals, nutrients, suspended particulate matter, and salt) in lakes and relatively small coastal areas but not for such a large and complex system of interconnected basins as the Baltic Sea. New morphometric data for the Baltic Sea and the defined subbasins and new hypsographic and volume curves based on digitized bathymetric data are also presented and used in this work. The aim is to present data on the fluxes of water to the system, precipitation, and the theoretical retention times for water and salt in the defined subbasins of the Baltic Sea, since those values provide fundamental information on how the system reacts to changes in, e.g., nutrient loading. The idea with this modeling approach, and the results presented in this work, is that these water fluxes, water retention rates, and the algorithms used to quantify vertical mixing and diffusion among the defined layers should be structured in such a manner that the model also can be used to quantify fluxes of nutrients and toxins. This places certain demands on the structure of the model that may be different from physical oceanographic models, e.g., in quantifying sedimentation, resuspension, mixing, and diffusion, and in the requirements regarding the accessibility of the necessary driving variables.