The Lužnice river is the backbone of the territory and drains a major part of the Třeboňská pánev Basin, and flows for 73.2 km within the PLA. Another larger river is the Nežárka, which drains the north-eastern section and flows for 28.5 km within the PLA. The Dračice and Koštěnický potok streams are the other significant water courses in the area.
The Třeboňsko does not only have natural rivers - the region is also characterised by its complex network of artificial channels and canals, which serve to fill and empty the extensive fishpond network. Among the best known canals are the Zlatá stoka (‘Golden canal’) and the Nová řeka (New River). The Zlatá stoka canal serves as a source of water supplying the fishponds of northern and central Třeboňsko and is 45 km in length. The Nová řeka at 14.5 km has the main function of directing part of the floodwaters from the Lužnice river into the Nežárka and also helps to protect the rybník Rožmberk (fishpond). The Rožmberk fishpond with an area of 490 ha is the largest of the 465 fishponds within the Třeboňsko PLA/BR.