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Two important communities related to oceanography in the Baltic Sea are those working on operational oceanography and Earth system science, with focusing on the same water body but different temporal scales. They have been coordinated through two organizations/programs: the Baltic Sea Operational Oceanographic System (BOOS) and the Baltic Sea Experiment (BALTEX) and its successor, the Baltic Earth Program (Earth system science for the Baltic Sea region), respectively. Although the two communities have archived significant progresses in their own fields since early 1990s, there were few interactions between the communities. Rapid advancements of operational oceanography on ocean monitoring, data sharing, modelling and historical ocean state reconstruction in the last decade have provided a wide range of data, products and modelling tools which may be used in Earth system and climate change research. This is especially true when operational oceanography in the Baltic Sea is in a transition to a seamless service, i.e., from basin to local scales, from synoptic to climate scales and from physical to biogeochemical and biological systems. On the other hand, the Baltic Sea Earth system research can help to improve operational oceanography by contributing research observations and transferring their research achievements to the operational system. Based on a review of state-of-the-art of BOOS monitoring and modelling capabilities and on-going BOOS research, this paper will highlight topics and areas which are related to the Baltic Earth Grand Challenges, i.e., salinity dynamics, land-sea biogeochemical linkages, natural hazards and extreme events, sea level dynamics, coastal morphology and erosion, regional variability of water and energy exchanges, and multi-drivers of regional Earth system changes. Potential win-win cooperation and interaction between the BOOS and the Baltic Earth communities are also proposed and discussed.