The autotrophic Baltic Sea acts as a sink for atmospheric CO2, however it is also characterised by nitrogen limitation and nitrogen accumulation, the latter indicating heterotrophy. Physical and biogeochemical processes generate this paradox, since the developments of the seasonal thermocline, the spring bloom and the riverine nitrogen inputs start during early spring. The Baltic Intermediate Water (BIW) is separated from the above surface layer, i.e., from the euphotic zone preventing a significant amount of the former winter mixed layer nitrogen from being used by phytoplankton, which finally becomes nitrogen limited. The deepening of the mixed layer in autumn reintegrates the nitrogen constrained within the BIW into the surface layer. Nitrogen in turn accumulates over an annual time scale depending on the riverine nitrogen loads. The temporal nitrogen enclosure in the BIW buffers the potential impact of nutrient inputs on the Baltic Sea and its trophic state.