The Younger Dryas-Holocene transition represents a period of significant thermal change, comparable in magnitude to modern warming, yet in a colder context and without the effect of anthropogenic disturbance. This is useful as a reference to tackle how biodiversity is affected by temperature in natural conditions. Here, we addressed the thermal change during this period in a southern Baltic coastal lake (Konarzewo Lake, Poland), as inferred by chironomid remains. We evaluated changes in chironomid communities and used Hill numbers to explore how commonness and rarity underlie biodiversity changes attributable to warming. We found evidence of warming at Konarzewo Lake during the Younger Dryas-Holocene transition, with inferred temperatures in the Younger Dryas period supporting the NW–SE gradient in Younger Dryas summer temperatures across Europe. Chironomid communities drastically changed during the thermal transition. However, Hill numbers showed no response to temperature when rare morphotypes were emphasized (order q = 0) or a weak response when they were balanced with common morphotypes (order q = 1). Hill number of order q = 2, emphasizing the most common morphotypes, consistently increased with temperature across different sample sizes or coverages. This illustrates how common morphotypes, rather than the rare ones, may boost biodiversity facing warming.