We present results from the assimilation of observed oceanic 3-D temperature and salinity fields into the global coupled Max Planck Institute Earth system model with the SEIK filter from January 1996 to December 2010. Our study is part of an effort to perform and evaluate assimilation and prediction within the same coupled climate model without the use of re-analysis data. We use two assimilation setups, one where oceanic observations over the entire water column are assimilated, and one where only oceanic observations below 50 m depth are assimilated. We compare the results from both assimilations with an unconstrained control experiment. While we do not find significant improvements due to assimilation in terms of the root-mean-square error of simulated temperature, 0–700 m heat content, sea surface height (SSH), and the Atlantic meridional overturning circulation (AMOC) against observations, we find the variability in terms of correlation with observations significantly improved due to assimilation, most prominently in the tropical oceans. Improvements over the control experiment are stronger in the sub-50 m assimilation experiment and in integrated quantities (SSH, AMOC).