Arctic aquatic systems are considered to be especially sensitive to anthropogenic disturbance, which can have cascading effects on biological communities as aquatic food-web structure is altered. Bio-indicators that respond to major limnological changes can be used to detect and infer major environmental change, such as climate warming, with the use of paleolimnological techniques. A multiproxy approach was used to quantify recent environmental changes at Baker Lake, Nunavut, Arctic Canada. Analyses of fossilized remains of chironomids and diatoms were conducted on a sediment core of 20 cm in length sampled at 0.5-cm intervals. A new surface sediment training set of subfossil chironomid assemblages from 65 lakes across the eastern Canadian Arctic generated a robust (r jack 2 = 0.79) surface water paleotemperature transfer function. The transfer function was applied to stratigraphic intervals from the Baker Lake sediment core to generate a paleotemperature reconstruction of sub-decadal resolution. The surface water temperature reconstruction inferred a 2°C increase in mid-summer surface water temperature for Baker Lake over the last 60 years, which was corroborated by the local instrumental record spanning the period of 1950-2007 AD. The chironomid record shows a recent decline of several cold-water taxa and appearance of warm-water indicators. This shift in community structure began circa 1906 AD, and intensified after 1940 AD. The corresponding fossil diatom record showed an increase in small planktonic Cyclotella taxa over the past 60 years, intensifying in the last 5 years, which also suggests a warmer climate and longer ice-free periods. The shifts in the diatom assemblages began later than the shifts in the chironomid assemblages, and were of lower magnitude, reflecting differences in the mechanisms in which these two indicators respond to environmental change.