Long-term monitoring of lakes and fjords on the northern coast of Ellesmere Island, Nunavut, provides information on the effects of climate change on these ecosystems and their seasonal and interannual dynamics. A 2-year, high-frequency record was obtained with a mooring installed in the deepest point of Ward Hunt Lake. This mooring installed in the deepest section of Ward Hunt Lake (Ward Hunt Island) allowed comparison of the seasonal dynamics of water temperature, chlorophyll fluorescence and dissolved oxygen concentrations between a year where the ice cover completely disappeared (2016) and years where it remained (2017-2019). This dataset is a contribution to the NEIGE program (Northern Ellesmere Island in the Global Environment).