The Baltic Nest Institute (BNI) at Stockholm University Baltic Sea Centre uses numerical modeling to provide scientific advice for management of Baltic Sea environment. Until several years ago, the sole focus was on open sea conditions, but a few years ago we intensified development of modeling tools for understanding of coastal ecosystems. A high resolution of the near-shore coastal ecosystems is vital to understand the feedback loops of carbon and methane during climate change as well as for understanding how the ecosystem responds in terms to the already observed temperature changes. There are also important management applications by analyzing the development of the environment of the archipelagos and coasts were the public meets the Baltic Sea. The combination of short temporal and small spatial scales require hydrodynamic modeling on very high resolution in the coastal area of interest, while the boundaries are strongly coupled to basin wide processes and therefore a nested approach with several models is required. Modeling of the coastal ecosystem will require new developments as most models of, e.g., eutrophication effects, have been developed on a large scale at deep waters with little or no feedback from biota on the sea floor. Intensive development of new ecological components has started at BNI in collaboration with Tvärminne Zoological Station, University of Helsinki, as well as with relevant departments at Stockholm University. BNI has developed hydrodynamic modeling systems that accurately simulates the physics in complex coastal areas. One application is tracing the river plume of the Öre river in northern Sweden and another is reproducing the penetration of upwelling in combination with local river supply in the complex archipelago setting of the Storfjärden + Pojo bay area in southwestern Finland. Modelling of the Storfjärden + Pojo Bay has been continued in 2022 to study dynamic of the near bottom water to determine areas where high concentration of methane can be expected. These results were helpful during a research cruise to study a methane dynamic in the Tvärminne area in August 2022. We also started a study of hydrodynamic processes in the Himmerfjärden which will be used in conjunction with the long term monitoring program performed by the Stockholm University in the Himmerfjärden area. The results will be most valuable for understanding of climate dynamics and, in a longer perspective, management of our coastal areas.