The system of natural surface waters in Šumava NP forms a spring area and peat bogs, a network of water courses and glacial lakes. This system is completed by artificial waterworks, including shipping canals, water races and artificial reservoirs (formal shipping, fish farming and dams).

The whole territory of Šumava National Park is included in the Protected Area of Natural Water Accumulation (CHOPAV), which almost corresponds with the boundaries of Šumava PLA (Government Regulation No. 40/1978), in accordance with Act No. 138/1973 Coll. on Water. The Protected Area of Natural Water Accumulation (CHOPAV) implements protective measures to prevent the reduction in the water potential of the territory, adverse changes in water quality and interference into natural conditions that could adversely affect the functioning of water resources in the territory (natural retention capacity and a potential source of drinking water).

The total average drainage from the area of Šumava NP is 1č.1 m3/s of which 61 % of the stated quantity drains into the Otava River due to the higher specific drainage level from the drainage area. The drainage from Šumava NP is 4.6% to the total drainage from the drainage area of the River Elbe, while the catchment area of Šumava NP represents only 1.4 % of the total Elbe drainage area in the CR. This documents the importance of this territory as a source region, where the specific drainage reaches more than three times the average value of the specific drainage from the entire drainage area of the River Elbe. Favourable climatic conditions and natural conditions, with plenty of wetlands and peat bogs, positively affect the accumulation of water in the area and regulate drainage. This is proven by the low fluctuation of the outflows from the territory, which is 1:15.

From the hydrology aspect, most of the drainage area belongs to the North Sea, and to the watershed of the River Elbe with the main Vltava and Otava rivers. Only a small area of the territory on the state border falls into the Danube watershed, which flows into the Black Sea - this is the watershed of Řezná near Železná Ruda, Malá Řezná near Medvědí hora (Bear Mountain), watershed of Čertova voda and Červený stream at Borovoladsko. The two largest rivers in Šumava spring in the Šumava plains in the central part of the mountains, where there are a number of raised bogs. The Otava River drains the western part of Šumava NP. The river is a confluence of two major rivers - the Vydra and the Křemelná. Their lower sections create canyons and steep valleys through the erosion process. The upper parts of their courses and particularly the tributaries of these rivers, flow through more shallow valleys in the Šumava countryside - whether it is the source of the Vydra River, the confluent at Modrava - Modravský, Roklanský and Filipohuťský streams or the major Křemelná - Slatinný tributaries and Prášilský streams. The Vltava River diverts the water from the south part of the NP and springs, like the Černý potok (Black stream), at the eastern slope of Černá hora (Black Mountain). After its confluence with the Vltavský stream near Borové Lady it becomes Teplá Vltava, while collecting further tributaries (the most abundant is Řasnice) and from the Černý Kříž, after the confluence with Studená Vltava, its freely meandering stream arrives near Želnava. This is also the location of the Lipno reservoir, the largest artificial waterworks in the territory.

Artificially created stagnant water, in addition to the aforementioned dam, is limited to a few former shipping reservoirs which are no longer used for this purpose (Žďárské Lake, Horní Polecká Nádrž, Tokaniště, Tišina and others). Small ponds (or firewater supplies) are located near villages (Modrava, Kvilda, České Žleby).

Besides natural water flows, there are also artificially created canals and raceways. In the west, there is the Vchynicko-Tetovský shipping canal, which draws a significant amount of water from the Vydra River above Antýgl and serves the needs of the power plant at Čeňkova Pila. The Schwarzenberg canal in the south of Šumava NP, which used to link the watersheds of the Elbe and the Danube, is now almost unfunctional. Further artificial water courses include the derivation canals (MVE) on the rivers Teplá, Studená Vltava and Losenice.

The natural glacial lakes, occurring at an altitude of about 1.000 m are a specific hydrological feature of Šumava. Their status is currently influenced by the degree of acidification due to the acid deposition and natural conditions of the lakes.

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