Originally, the marshy Zwin area was mostly settled by shepherds and fishermen. With the encouragement of the Counts of Flanders, several dikes were built between the 11th and the 13th century and the land successfully dewatered, giving rise to agriculture and further sheep breeding. New parishes were founded and the early settlement of Sint-Anna-ter-Muiden, later made part of Westkapelle, obtained city rights in 1242.
The strategic importance of the Zwin harbour came to light in 1301, during the war between Count Guy of Dampierre and the French King Philip the Fair. During the Hundred Years' War that followed shortly after, several battles were fought between France and England for supremacy of the area including the Battle of Sluys in June 1340. The local population tried to remain neutral as it was politically tied to Flanders, then allied to France, but economically dependent on wool from England. Under Philip the Bold’s leadership, it took advantage of the relative peace of the end of the century to fortify the canal linking the Zwin to the port of Bruges.
The beginning of the 15th century witnessed several renewed English attacks on neighboring Sluis, with devastating effects on the local economy, until a lasting peace was signed in 1439. The end of the century was marked by internal rebellions against Maximilian of Austria and strategic flooding of the polders. The reign of Charles V in the following century saw peace coming back to the region. This was also the time when the Zwin started silting and when apple orchards were planted to supplement the local economy.
The Wars of Religion of the late 16th century brought renewed floods and devastation, but the economy managed to come back to life after the Peace of Westphalia with the cultivation of rapeseed and potatoes. The strength of this agricultural rebirth and of the cattle trade allowed the local farmers to weather future economic crises relatively well.
Following the Treaty of Utrecht in 1713, the territory of Knokke was annexed to the Netherlands, but the old border was reestablished at the Zwin a few years later. After the Battle of Fleurus (1794), Bruges, Knokke and the neighboring municipalities were included in the department of the Lys. The construction of the Leopold Canal in 1857 made the closing of the Zwin and its transformation in a natural reservation possible. The development of Knokke and Heist as tourist destinations followed soon after. The population of Knokke doubled between 1873 and 1914 to 3,326 inhabitants, then again from 1914 to 1930 and again to reach more than 14,000 in 1965 despite the heavy setbacks brought by World War II.