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SANIFS (Southern Adriatic Northern Ionian coastal Forecasting System) is a coastal-ocean operational system based on the unstructured grid finite-element three-dimensional hydrodynamic SHYFEM model, providing short-term forecasts. The operational chain is based on a downscaling approach starting from the large-scale system for the entire Mediterranean Basin (MFS, Mediterranean Forecasting System), which provides initial and boundary condition fields to the nested system.<br><br> The model is configured to provide hydrodynamics and active tracer forecasts both in open ocean and coastal waters of southeastern Italy using a variable horizontal resolution from the open sea (3–4 km) to coastal areas (50–500 m).<br><br> Given that the coastal fields are driven by a combination of both local (also known as coastal) and deep-ocean forcings propagating along the shelf, the performance of SANIFS was verified both in forecast and simulation mode, first (i) on the large and shelf-coastal scales by comparing with a large-scale survey CTD (conductivity–temperature–depth) in the Gulf of Taranto and then (ii) on the coastal-harbour scale (Mar Grande of Taranto) by comparison with CTD, ADCP (acoustic doppler current profiler) and tide gauge data.<br><br> Sensitivity tests were performed on initialization conditions (mainly focused on spin-up procedures) and on surface boundary conditions by assessing the reliability of two alternative datasets at different horizontal resolution (12.5 and 6.5 km). <br><br> The SANIFS forecasts at a lead time of 1 day were compared with the MFS forecasts, highlighting that SANIFS is able to retain the large-scale dynamics of MFS. The large-scale dynamics of MFS are correctly propagated to the shelf-coastal scale, improving the forecast accuracy (+17 % for temperature and +6 % for salinity compared to MFS). Moreover, the added value of SANIFS was assessed on the coastal-harbour scale, which is not covered by the coarse resolution of MFS, where the fields forecasted by SANIFS reproduced the observations well (temperature RMSE equal to 0.11 °C).<br><br> Furthermore, SANIFS simulations were compared with hourly time series of temperature, sea level and velocity measured on the coastal-harbour scale, showing a good agreement. Simulations in the Gulf of Taranto described a circulation mainly characterized by an anticyclonic gyre with the presence of cyclonic vortexes in shelf-coastal areas. A surface water inflow from the open sea to Mar Grande characterizes the coastal-harbour scale.