The climate at Payún Matrú is cold and dry with strong westerly winds. Annual temperature varies between while the average temperature in the wider region is about and the average annual precipitation amounts to . Generally, the area of Payún Matrú is characterized by a continental climate with hot summers especially at lower elevations and cold winters especially at higher elevations. The climate is dry owing to the rainshadow effect of the Andes which block moisture bearing winds from reaching Payún Matrú, and strong winds and the evaporation associated with them reinforce the dryness. In the westerly part of the volcanic field most precipitation falls during winter under the influence of the Andes, while the eastern part has most precipitation occurring during summer. The higher parts of Payún Matrú may have risen above the snowline during ice ages, and periglacial landforms have been observed. Palynology data from south of the region indicate that the climate has been stable since the Late Pleistocene.