Through the last millennium, Patagonia has been affected by changing climate conditions and successive volcanic eruptions. Lake Tonček is a high-altitude lake in the Southern Volcanic Zone in the northern Patagonian Andes. We documented the responses of the subfossil chironomid community to the effects of successive volcanic and different conditions in a sedimentary sequence from this lake comprising the last 900 years. The community composition and structure (abundance, diversity, and richness) and the development of morphological anomalies in the chironomid mouthparts were evaluated throughout the core. Both climatic conditions and volcanism affected the chironomid community differentially. The chironomid community changed following short-term climate change patterns, being affecting not only by temperature changes but also by variations in the regional precipitation regime. Decreases in abundance and diversity were only observed in coarse volcanic layers. In these samples, we recorded a high percentage of damaged chironomid mouthparts caused by mechanical wear, breakage or abrasion, possibly due to the increase of mineral particles. Our results represent important baseline data about the responses of chironomid communities to environmental disturbances in high-altitude lakes over long time frames.