This study presents the Late-Holocene evolution of a northern Southampton Island (Nunavut, Canada) lake, using fossil chironomids supported by sedimentological evidences (XRF, grain size and CNS). All proxies revealed a relatively stable environment during the last millennium with short-lived events driving changes in the entire lake ecosystem. The chironomid-based paleotemperatures revealed variations of significant amplitude coincident with changes in the sediment density and chemical composition of the core. Higher temperature intervals were generally correlated to lower sediment density with higher chironomid concentration and diversity. Higher temperatures were recorded from cal yr AD 1160 to AD 1360, which may correspond to the Medieval Warm Period. Between cal yr AD 1360 and AD 1700, lower temperatures were probably related to a Little Ice Age event. This study presents new information on the timing of known climatic events which will refine our knowledge of the paleoclimate and climatic models of the Foxe Basin region. It also provides a new framework for the evolution of such freshwater ecosystems under the “Anthropocene” and underlines the importance of including sedimentological proxies when interpreting chironomid remains as this combined approach provides an extended overview of the past hydrological and geochemical changes and their impacts on lake biota.