Coastal zones are among the most variable environments. As such, they require adaptive water management to ensure the balance of economic and social interests with environmental concerns. High quality marine data of hydrographic conditions e.g., sea level, temperature, salinity, and currents are needed to provide a sound foundation for the decision making process. Operational models with sufficiently high forecasting quality and resolution can be used for a further extension of the marine service toward the coastal-estuary areas. The Limfjord is a large and shallow water body in Northern Jutland, connecting the North Sea in the West and the Kattegat in the East. It is currently not covered by the CMEMS service, despite its importance for sea shipping, aquaculture and mussel fisheries. In this study, we use the operational HIROMB-BOOS Model (HBM) to resolve the full Baltic-Limfjord-North Sea system with a horizontal resolution of 185.2 m in the Limfjord. The study shows several factors that are essential for successfully modeling the coastal-estuary system: (a) high computational efficiency and flexible grids to allow high resolution in the fjord, (b) an improved short wave radiation scheme to model the thermodynamics and the diurnal variability of the temperature in very shallow waters, (c) high resolution atmospheric forcing, (d) adequate river forcing, and (e) accurate bathymetry in the narrow straits. With properly resolving these issues, the system is able to provide high quality sea level forecast for storm surge warning and hydrography forecasts: temperature, salinity and currents with sufficiently good quality for ecosystem-based management. The model is able to simulate the complex spatial and temporal pattern of sea level, salinity and temperature in the Limfjord and to reproduce their diurnal, seasonal and interannual variability and stratification rather well. Its high computational efficiency makes it possible to model the transition from the basin-scales to coastal- and estuary-scales seamlessly. In total, The HBM model has been successfully extended, to include the complex estuary system of the Limfjord, and shows an adequate model performance with regards to sea level, salinity and temperature predictions, suitable for storm surge warning applications and coastal management applications.