Šumava is located within the area of a transitional Central European climate and according to the climatic map of the CR; the main mountain territory belongs to the cold climate area. The local climate is transitory, with oceanic and continental climate influences, i.e. throughout the year; there are only slight temperature variations and relatively high rainfall.

The temperature gradient is especially changing with the altitude (the average temperatures are approximately 6° C at an altitude of 750 m.a.s.l. and at an altitude of 1.300m.a.s.l. are about 3 ° C), but in terrain depressions and mountain valleys (e.g., the hill course of the Vltava and the Otava), the temperatures are influenced due to temperature inversion and are significantly lower than at the mountain peaks and ridges, i.e. above the inversion. The coldest month is usually January and the warmest is usually July. The period with average temperature <- 0 ° C starts at the highest altitudes in early November (late October) and finishes in late March, or in April (winter lasts five months, although the morning frost remains for another two months).

Total rainfall also increases with an increasing altitude, while the highest levels are detected in the central part of Šumava (Březník 1486-1552 mm on a thirty-year average) and of course this varies at the windward and leeward sides of the mountain.

The vegetation development is considerably influenced by the quantity of the snow and by how long the snow cover lasts. The quantity of the snow is influenced by the altitude and by mesorelief (most snow is in the highest altitudes of the border mountain ridge; the least snow falls on the north-east edge of Šumava). A permanent snow cover lies in the highest altitudes for 120-150 days (at the top of the Großer Arber for about 200 days a year). Moving snow (avalanches, creeping snow) which affects the formation of the vegetation, can only be found on the glacial cirque walls.
The highest points and the areas with temperature inversions are heavily affected by fog and the mountain ridges are affected by wind and frost.

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