Třeboňsko is one of few Czech PLAs designated in a flat landscape that has been influenced by man for hundreds of years. Despite this, exceptionally significant natural treasures have been preserved here. A large part of the area  is formed by a balanced landscape where human activity is in harmony with nature. Třeboňsko was therefore designated one of six Czech UNESCO MAB biospheric reserves in 1977. 

Man has influenced Třeboňsko landscape formation since the 12th century. Man has particularly adjusted the wetland water system, resulting in the  formation of an ingenious network of artificial sewers (for example Zlatá Stoka and Nová Řeka) and a large number of ponds. That is why Třeboňsko is the centre of Czech pond culture (There are 460 ponds in total). This large pond network together with secondary formed littoral coenoses has initiated a significant breeding site and migration stop for water birds. The area is significant for its rich wetlands and water vegetation.

The most significant biotopes are represented by large transitional bogs with preserved phytocoenoses (Pinus rotundata bog forests) and the invertebrates dependent on it. A large area  of the original meandering parts of rivers (for example Lužnice River) has also been preserved, as well as alluvial plains, remnants of alluvial forests and extremely xerid sites of airborne sand. Two wetlands (Třeboňské Rybníky and Třeboňská Rašeliniště) of international significance protected by the Ramsar convention have been designated here.

The area is significant with regard to the conservation of a range of endangered vulnerable vertebrates, for example lutra lutra (otter) and Haliaeetus albicilla (white-tailed eagle). The balanced natural elements of the landscape are well accompanied by quite rare settlements and unique preserved historical architecture in towns (Třeboň Town Monument Reserve) and villages. With regard to natural and cultural factors, Třeboňsko is an exceptional area in the European context and  has also significant recreational use. Traditionally, wetland ecological research (by the Institute of Botany, Academy of Sciences of the Czech Republic) is conducted here. Recently, Třeboňsko was included in the international network of objects of long-term ecological research (ILTER).