Considering a high proportion of grassland areas in mountain and upland regions, the agro-environmental problems there relate mainly to the management of meadow phytocoenoses and its impact on individual components of the environment. The proposed system of agro-environmental measures is limiting the sources of harmful emissions from grassland farming with the aim to improve the protection of air, water, wetlands, soils and biodiversity. In spite of decreased livestock population, the limitation of risks from air pollution concerns mainly the fertiliser application systems, the animal grazing and housing systems, as well as the excreta application and manipulation techniques. The risk of surface water pollution is connected especially with the fertiliser application to grassland and to arable land, and also with the erosion. Specifying a suitable date for fertiliser application and leaving empty spaces – so called distance bands – during fertilisation are some of the most important measures. A careless application resulting in an escape of liquid manure or slurry is one of potential risks of surface water pollution and must be avoided by improved technology and better labour control and work discipline. The potential risks for surface water induced by erosion or run-off are lower at the sites with a mosaic structure. The conservation of large wetlands having non-production functions is performed in compliance with the rules for protection of surface waters. Smaller wetland areas (less than 100 m2) at meadows and pastures could be left to overgrow with hygrophilous woody plants or planted with the local wood species in such a way that the grazing animals would walk around these coppices.