HEP's thermal power plants are located in urban or industrial areas and not within the Natura 2000 ecological network or areas protected at national level. Some protected areas are close to generating facilities, i.e. TE-TO Zagreb CHP is close to the significant landscape Savica or TE-TO Osijek CHP is close to the border of the Mura-Drava Regional Park. A large number of HEP's hydro power plants are located within the Natura 2000 ecological network and some are wholly or partly located in protected areas such as national parks, nature parks, regional parks and areas of significant landscape. Also, just over 5,000 kilometers of medium voltage overhead lines are located within the Natura 2000 bird conservation area, which accounts for about 20 percent of the total length of HEP ODS's MV overhead lines.
During 2018, there were no pollution, construction or expansion of any plant, impacts on the spread of invasive species, pathogens or parasites, reduction in the number of indigenous species, changes in habitats, changes in natural processes and changes in groundwater salinity or level.
In protected areas, HEP has to plan and construct such energy infrastructure that prevents and minimizes the risks for birds residing in these areas. Areas of ecological network have been identified as well as associated species for which the areas have been defined. Protection measures cover 17 bird species from the Red List of Endangered Bird Species.
In 2018, as part of an agreement signed with the Ministry of the Environment and Energy on the protection of white storks, HEP ODS installed new supports for stork nests on distribution network towers and poles and repaired and disposed of worn-out ones. With 60 implemented protection measures, Elektra Križ excels among the 14 distribution areas on the territory of which white storks nest.
Since 2014, when an artificial island was built on the Varaždin HPP reservoir, the BIOM Association has been maintaining the island without vegetation in order to preserve favorable conditions for nesting of common tern (Sterna hirundo). In the fall and early spring, before the terns return from places they spent their winter, the vegetation is mowed and removed from the island. The succession of islands and sandbanks severely degrades such habitats of crucial importance for these birds. As of September 2017, BIOM has been implementing this activity as part of the Interreg ČIGRA project - Conservation of Tern Populations in the Sava and the Drava River Basins, launched by the Institute for Ornithology of the Croatian Academy of Sciences and Arts, with partners from Croatia and Slovenia. The Association installed photo traps on the island to monitor tern nesting, as well as the presence of other birds and predators such as otters. Due to pronounced predation of otters on tern eggs and young terns, an electrical fence was erected as part of the Interreg Project to prevent the otters from coming to the island and make tern nesting more successful. Apart from conservation activities, the Association has organized and conducted a seven-day educational camp “Our Drava” for high school students from Varaždin County, which included a visit to the Čakovec HPP. The main themes of the camp were common terns, biodiversity and protection of the Drava River.