The climate of the south-western part of Macedonia where Pelister Mountain is located can be characterized as moderate continental. However, because Pelister National Park is situated at altitudes higher than 891 m above the sea level its local climate is typically mountainous. The winters are long, cold and with lots of snowfalls, whereas the summers are short and rather cold. January and February are the coldest months whereas July and August are the warmest. The precipitation is highest in October and December, but there is another peak in May. The precipitation during the summer season accounts for 16.5% of the annual amount. The snow cover stays from November to April, in the higher parts to May, and in small remnants up to June. The data on precipitation levels and temperature in Pelister National Park are available only for the period from 1934 to 1940 when there was a weather station in the Park.

The bedrock in Pelister National Park is primarily Paleozoic and Mesozoic in age, with few glacial and fluvioglacial overlays dating from Quaternary. Among the Paleozoic rocks, the series of green shale are the oldest and most ubiquitous stratigraphic unit. Typical for the Park is the “Pelister Granite”, Paleozoic alkaline-granite dating from the Ordovician, some 456 millions years ago, and usually embedded within the Paleozoic shale. Other Paleozoic rocks found in the Park include quartz- and quartz-sericite schists. The gabbro is the most ubiquitous among the Mesozoic rocks, found in several places, including a large mass with a surface area of 5 km², situated south-east of the village of Malovishta. Other Mesozoic complexes are also found, such as diabase and mermekitic granite and dolerite veins. Due to the nature and compactness of the bedrock as well as the vegetative cover and lack of human activities the erosion in the Park is negligible.