The use of sea surface height (SSH) measurements by altimeter satellites in the Mediterranean requires an accurate mean dynamic topography (MDT) field with a high horizontal resolution which must be added to observations. This study presents a new Mediterranean MDT estimate calculated from the diagnostics of an existing operational assimilation system in the Mediterranean. The calculation starts from the assumption that the error in the MDT field appears in the assimilation system as a temporally constant and spatially variable observational bias. Therefore, we can reduce this error by calculating long-term averages of dynamic topography departures and by subtracting them from the previous MDT field. The analysis system statistics show that the assimilation of the SSH in the Mediterranean is more accurate with the new MDT estimate.