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The decision to build a new waterway (strait) in the Polish part of the Vistula Spit was made in 2017. The new connection between the Gulf of Gdańsk and the Vistula Lagoon is planned as an artificial navigable channel with a lock and a small port. During storm surges and wind tides in the gulf or in the lagoon, sluicing will be required for vessels to tackle the Vistula Spit. This procedure does not require significant water flow through the channel in normal conditions. However, in the case of a lock failure or in the case of controlled opening of the gate to increase water exchange in the lagoon or to reduce flood risk in the Vistula Lagoon, high flow rates may occur in the navigable channel and in the neighboring port basin. In order to inves-tigate the hydraulic conditions in such extraordinary situations, numerical modeling of the hydrodynamics during water damming in the gulf or in the lagoon is performed. To analyze the hydrodynamics of the artificial connection between the sea and the lagoon during periods of high water stages, mathematical modeling is required. This paper presents the shallow water equations (SWE) model adapted to simulate the flow through the port basin and the navigable channel. The calcula-tions allowed the relation between the water head and the capacity of the navigable channel to be found, as well as to analyze circulations which may occur in the port basin.