The biodiversity of shallow (zmax <5–7 m) lakes is sensitive to water-level and climate changes, but few such aquatic ecosystems have been studied in the context of quantitative climate reconstruction. Lac Lili (unofficial name) is located in the boreal forest of western Quebec, Canada, and was chosen for its shallowness (zmax = 1.40 m) to assess if chironomid assemblages in the sediments could be used to reconstruct Holocene temperature fluctuations quantitatively. Inferred temperatures displayed a decreasing trend from a maximum value ca. 8000–3500 cal year BP, slight warming between ca. 3500 and 3000 cal year BP, followed by cooling to the present. Although chironomid assemblages were influenced by factors other than climate, primarily water depth and changes in macrophyte richness, the reconstructed Holocene temperature pattern was very similar to the known regional climate history. Temperature inferences derived from the chironomid assemblages were, however, warmer than the two reference periods. This deviation was likely a consequence of three factors: (1) shallowness of the lake, which favoured littoral taxa with warmer-than-today temperature optima, (2) the low number of lakes warmer than 16°C in the training set, and (3) the absence of shallow lakes in the training set.