In this study we examine pools of carbon (C), nitrogen (N), and phosphorus (P) in the Baltic Sea, both simulated and reconstructed from observations. We further quantify key fluxes in the C, N, and P cycling. Our calculations include pelagic reservoirs as well as the storage in the active sediment layer, which allows a complete coverage of the overall C, N, and P cycling on a system-scale. A striking property of C versus N and P cycling is that while the external supplies of total N and P (TN and TP) are largely balanced by internal removal processes, the total carbon (TC) supply is mainly compensated by a net export out of the system. In other words, external inputs of TN and TP are, in contrast to TC, rather efficiently filtered within the Baltic Sea. Further, there is a net export of TN and TP out of the system, but a net import of dissolved inorganic N and P (DIN and DIP). There is on the contrary a net export of both the organic and inorganic fractions of TC. While the pelagic pools of TC and TP are dominated by inorganic compounds, TN largely consists of organic N because allochthonous organic N is poorly degradable. There are however large basin-wise differences in C, N, and P elemental ratios as well as in inorganic versus organic fractions. These differences reflect both the differing ratios in external loads and differing oxygen conditions determining the redox-dependent fluxes of DIN and DIP.