We generate a multi-proxy sub-centennial-scale reconstruction of environmental change during the past two millennia from Itilliq Lake, Baffin Island, Arctic Canada. Our reconstruction arises from a finely subsectioned 210Pb- and 14C-dated surface sediment core and includes measures of organic matter (e.g., chlorophyll a; carbon–nitrogen ratio) and insect (Diptera: Chironomidae) assemblages. Within the past millennium, the least productive, and by inference coldest, conditions occurred ca. AD 1700–1850, late in the Little Ice Age. The 2000-yr sediment record also reveals an episode of reduced organic matter deposition during the 6th–7th century AD; combined with the few other records comparable in resolution that span this time interval from Baffin Island, we suggest that this cold episode was experienced regionally. A comparable cold climatic episode occurred in Alaska and western Canada at this time, suggesting that the first millennium AD cold climate anomaly may have occurred throughout the Arctic. Dramatic increases in aquatic biological productivity at multiple trophic levels are indicated by increased chlorophyll a concentrations since AD 1800 and chironomid concentrations since AD 1900, both of which have risen to levels unprecedented over the past 2000 yr.