The accelerating sea-ice, ice sheet and glacial melt associated with climate warming have resulted in important changes in the Arctic region over the past decades. In northern Baffin Bay, the formation of the North Open Water (NOW) polynya, which is intrinsically linked to regional sea-ice conditions and ocean circulation, has become more variable in recent years. To understand how climate-driven changes affect sea-surface conditions in the polynya, we analyzed dinoflagellate cyst assemblages from a sediment core record that covers the past ca. 3800 years, and developed an index based on the locations of modern analogues from a large regional reference dataset. Our results suggest a prolonged open-water season characterized by higher summer sea-surface salinity and temperature between ca. 3800 to 2500 years BP, followed by gradual cooling, freshening and increased sea-ice influence from 2500 to 1500 years BP, and continued sea-surface cooling with a shorter open-water season from 1500 to 156 years BP. The modern warming translates into a rapid turnover in the composition of dinoflagellate cyst assemblages during the last 50 years of our record, unprecedented for at least the past 3800 years studied here. For the uppermost part of our core (ca. 2009 to 2015 CE), the dinoflagellate cyst assemblages suggest increased stratification and sea-surface freshening resulting from increased glacial runoff and Arctic sea-ice export into the NOW region. Arctic climate projections indicate accelerated sea-ice thinning and ice sheet melt in the future, pointing to a shorter polynya season and increased polar inflows leading to fundamental changes within the NOW polynya into future years.