Shkrel MNP is a noteworthy area with distinct ecological systems. The vertical zone that begins at the entrance of the park (250m) and goes up to its highest peak (Maja e Thatë, 2541m) makes it possible to have a great diversity of flora and fauna in this area. Species of national and international importance are present in the aquatic flora and fauna, as well as in the wetlands and terrestrial habitats of the park. The wide range of vegetation, altitude and geographic position make the park very rich the natural values it offers.
The MNP is also home to a limited population of SPECs (Species of European Concern). Large carnivores such as the brown bear (ursus arctos), the Balkan lynx (lynx lynx) and the wolf (canis lupus), along with large herbivores like the wild goat (rupicapra rupicapra) all call the park their home. Moreover, due to its distinct ecological conditions, the area itself is a natural habitat that can host a considerable number of these species.

There have also been sightings of the western capercaillie (tetrao urogallus), the griffon vulture (gyps fulvus), the peregrine falcon (falco peregrinus), and the common kestrel (alco tinnunculus) in the park area.

Field observations conducted in the area have revealed that the following habitat types can be found in Shkrel MNP:

  • Oriental hornbeam forests
  • Thermophilous beech forests
  • Montane and subalpine beech forests
  • Oak-hornbeam forests
  • Streams and rivers
  • Mountane grasslands
  • Dinaric Mountains mixed forests
  • Thermophilous grasslands and pastures;
  • Oro-Mediterranean rocky habitats, or rocky habitats of temperate zones.

The main vegetation levels are:

  • 200-900 mamsl - forests with mixed oak, hornbeam, ash, etc;
  • 900-1.400 mamsl - forests with beech, black pine and spruce;
  • 1800-2.400 mamsl - alpine vegetation and rocky meadow habitats.

The untouched beech can only be found atop the inaccessible peaks. Most of the remaining native forests hold Heldreich's pine (Pinus heldreichii) and are located mainly in the higher, hard to reach mountains.

The high mountains of the Shkrel MNP area represent the center of the Albanian flora endemism. These areas are of national, European, and international importance.

Different endemic plants can be found throughout Shkrel Park, making the protection of the environment here absolutely necessary in order to ensure their existence for future generations. Park species such as Wulfenia (Wulfenia Baldacci), Bellflower (Campanula albanica), Helleborus multifidus, and the Albanian lily (Lilium albanicum) account for 10 percent of all endemic species in Albania. The park is also rich in other flowers, 60 species of which can be found in local gardens and along various walking paths.

Among the endemic fauna and endangered species are: the green salamander (Aneides aeneus), the alpine newt (Ichthyosaurus alpestris), the griffon vulture (gyps fulvus), the booted eagle (Hieraaetus pennatus), the European badger (Meles meles), the wild alpine goat (Rupicapra rupicapra). Many of these species can only be found with little luck.

The medicinal and aromatic plants of the park include: sage (Salvia officinalis), chamomile (Anthemis nobilis), mountain tea (Origanum vulgare L.), summer savory (Satureja hortensis), lavender (Lavendula), gentian (Gentiana lutea), tilia (Tilia spp.), black juniper (Juniperus indica) and red juniper (Juniperus virginiana).