Ocean Dynamics (2019) 69:1217–1237 1235 below a specified depth, the assimilation was stabilised in the North Sea. However, in the Baltic, unrealistically high concentrations even appeared with a vertical localisation that only changed the upper 5 m (3 model layers). The results from the weakly coupled assimilation show that in the North and Baltic Seas the assimilation of only SST data can improve the oxygen concentrations. This improvement is even larger for the strongly coupled assimilation because of the correlation between temperature and oxygen concentrations. The effect on other BGC model fields was small, but there was no obvious deterioration. This is in contrast to other studies that performed physical data assimilation in the North Atlantic (Berline et al. 2007) or the California Current System (Raghukumar et al. 2015). The application of the strongly coupled assimilation with actual BGC concentrations showed that the cross- covariances between the SST and the BGC fields only lead to changes that were small compared to the errors in the BGC fields. The limited in situ data was not sufficient to provide a clear result whether the changes to the BGC fields are significant. The differences in the strongly coupled assimilation using actual concentrations compared to logarithmic con- centrations showed a clear advantage of actual concentra- tions. The assimilation using actual concentrations lead to a more stable assimilation process and more realistic model fields while with logarithmic concentrations unrealistic val- ues were obtained. The application of a vertical localisation leads to a clear improvement, but did not solve the issue of unrealistic concentrations in the Baltic Sea. Further, updat- ing only nutrients and oxygen improved the results. 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