From the viewpoint of nature conservation the protected landscape area and biosphere reserve are divided into three zones: the core zone (1st zone of PLA, core area BR), buffer zone (2nd zone of PLA, buffer zone BR) CHKO and transition zone (3rd zone of PLA, transition area BR).
The core zone (1) covering the area of 3,749 hectares includes the most valuable and least damaged part of the area, mostly additionally protected as a small-scale specially protected area, and it makes up 5.4 per cent of the area. All activities in the core zone have to be subordinated to the protection regime of the area in question. If it is the ecosystem stage conditioned by a certain human activity, it is necessary to maintain this activity in the form that enabled the valuable biotopes to come into being.
The buffer zone (2) covering the area of 35,879 hectares, serves as a zone eliminating negative influences of the surrounding areas, on the core zone. Its area makes up 50.3 per cent of the PLA/BR. Here, only such activities may be carried out that do not endanger the core zone. Into the bargain, there are usually research localities and experimental areas located in this zone that serve for the restoration of degraded ecosystems.
The transition zone (3) covering the area of 30,372 hectares, also serves for the protection of the central zone from outer influences, however, regulation measures here are more moderate than in the buffer zone, and it makes up 44.3 per cent of the PLA/BR.
Zoning of Třeboňsko PLA was approved by the Ministry of the Environment of the Czech Republic on 3rd October 1995 under No.: OOP/4976/95.
Small-scale specially protected areas
The most valuable parts of Třeboňsko PLA are protected in 31 nature reserves, 4 of them are in the top category of the national nature reserve, further there are 2 national nature monument, 18 nature reserves and 7 nature monuments.
At present there are over 200 trees protected by the state as monument trees in the territory of Třeboňsko PLA.
Wetlands of international importance
There are two areas in the Třeboňsko PLA/BR (consisting of a large number of partial localities) that were put on the list of wetlands of international importance protected by the Ramsar Convention.
Territorial system of ecological stability
From the viewpoint of territorial systems of ecological stability, 60 composition elements of regional and higher levels were determined in the territory of the PLA/BR. In comparison to other areas of this country, the existing skeleton of economic landscape stability in the territory of Třeboňsko PLA may be evaluated as satisfactory, which results from its large forested areas and, in general, a considerable percentage of natural and nature-close biotopes. The most important element here is the supra-regional bio-centre Stará řeka, involving a large part of the most valuable territory of the central Třeboňsko PLA, and the supra-regional bio-centre Červené blato with a large area covered by the bog pine. The third supra-regional bio-centre is the unique fen Ruda near Horusický rybník. Important supra-regional or regional bio-corridors are the Lužnice and Nežárka Rivers and their floodplains, and other important areas. Recently, the most valuable part of the CHKO/BR covering the area of 180 km2, was proposed as a bio-centre (core area) of Central European importance in the frame of the European EECONET network. The Birdlife International organisation has classified Třeboňsko PLA for years as an important European bird area (IBA - Important Bird Area).