The northeastern coastal plain of Belgium was a well-developed region during the late medieval period when Bruges and a series of smaller harbours became connected to the North Sea via the Zwin tidal channel. Yet, ecological data related to the evolution of the regional environment of the former Zwin region are still lacking. Diatoms, pollen, and macrobotanical remains have been studied for the first time from two cores drilled in the surroundings of the lost harbour of Hoeke. The sediments in both cores were deposited in four successive tidal channel systems spanning the pre-Roman to late medieval periods. Marine tychoplanktonic and planktonic diatoms were dominant and confirmed the presence of open marine tidal channels, while marine epipsammic diatoms were specific to channel deposits (systems 1 and 4) and marine epipelic diatoms characterised channel and accretion deposits (systems 2 and 3). The sediments of the late medieval Zwin main channel and tributary (system 4) are both characterised by marine tychoplanktonic and epipsammic species. The palynomorphs were typical of marine tidal deposits and (reworked) peat, while macroremains pointed to freshwater plants growing in the vicinity. The palynomorphs (system 4) suggest a more open landscape associated with the extensive reclamation and embankment of the Zwin region. Diatoms in the superjacent tidal deposits indicate that the late medieval Zwin silted up rapidly.