A combination of biotic, sedimentary and biogeochemical proxies was used to investigate the timing and causes of post-18th century changes in the stratigraphic record of a large, deep lake on the Boothia Peninsula, Nunavut, Canada (70 degrees 15' N, 94 degrees 30' W). A varve chronology verified with radioisotopic dating (Pb-210 and Cs-137) revealed a complex pattern of environmental dynamics since c. AD 1830. An increase in the diatoms Asterionella formosa, Stephanodiscus minutulus and Cyclotella atomus and a decrease in Aulacoseira taxa in the uppermost centimetre of sediment suggested that environmental conditions have favoured the growth of smaller and/ or lighter planktonic species since the 1980s. Longer term changes in some benthic species, the chrysophyte cysts to diatom valve ratio, %C, and C/N ratios suggest declined river inflow and a relative reduction in allochthonous inputs during the last century. Higher than average delta N-15 values in the late 19th to early 20th centuries coincide with changes in bulk carbon and nitrogen profiles, and below average values since approximately 1950 may be associated with increased atmospheric N loading or reduced productivity. Biogenic silica and organic carbon accumulation in the sediments suggest a possible decline in lake production during the 20th century that may be associated with changes in the river discharge regime. The short and long-term ecological and biogeochemical trends were also reflected in the sedimentary structure through declining varve thickness for the duration of the record and an abrupt change in sedimentology in the uppermost 1 cm, coinciding with deposition since ca. AD 1987. Together, these biological and physical changes suggest changes in hydroclimatic conditions in the 20th century, and an increase in planktonic diatom taxa since the 1980s that coincides with a distinct period of climate warming.