Nature 2000 sites are created in the aim of the conservation of rare and endangered plant and animal species (especially birds) and their habitats in UE. The protection of these areas depends on limi-tation of realization of projects that may significantly affect the environment related with intensive agricultural activity. In the range of agriculture-environment-climatical programme the agriculture may be development in the agritourism area and it also serves the protection of biodiversity by the protection of swamps and peatbog. In the Warmia and Mazury Region based on analysis of plans of protective tasks determined agricultural risks of the following natural habitats: meadow and grass – in appropriate management of meadows and grasslands peatbogs – meliorations old-river beds and water bodies – agricultural flows and breeding habitats of birds – agricultural intensification and che-micalization drying boggy terrains and burning meadows. The protection of these habitats mainly depends on the suitable use of meadow and grassland management and the limitation of agricultural intensification and chemicalization.