Prediction of hydrographic conditions e.g., sea level, temperature, salinity and currents in coastal-estuary continuum is the basis for climate change adaptation and mitigation and ecosystem-based management in coastal waters. In this study, we compare and develop two strategies: either use stand-alone Limfjord setup with boundary conditions from CMEMS or extend the CMEMS Baltic Monitoring Forecasting Centre (BAL-MFC) setup with a nested Limfjord domain. The resolution of Limfjord domain in about 185 m horizontal resolution. This domain is not covered by CMEMS, despite its importance for sea shipping, aquaculture and mussel fi sheries. The ocean model that is applied is the BAL-MFC HBM model (HIROMB-BOOS Model). The results show that both approaches are able to provide high quality sea level forecast for storm surge warning, temperature, salinity and currents with reasonably good quality for ecosystem-based management both for nested an stand-alone models. The models are able to handle the shallow thermoclines in summer as well as the strong tidal and wind driven transport through narrow straits in autumn and winter. Nested models usually have better performance and do not depend on possible change of CMEMS model that supplies boundary conditions. Nevertheless, stand-alone setup is attractive as it requires much less computational resources, can be tuned more effectively, less limits for increasing the resolution.