The territory of Shkrel MNP is entirely apart of the northern Albanian mountains, which are the southern part of the Dinaric Arc. The mountains are entirely made of black limestone mixed with silicon from the Upper Triassic, Lower Jurassic and Upper Jurassic geological periods. The altitude of the area is about 200m above sea level in the southwest part of the park and goes up to 2400m in the northeastern part. Vegetation cover varies significantly depending on the elevation. But across the park territory, the water shortage is quite clear given the geological formations, the specific quantities of annual rainfall and distribution throughout the year. The best visual representation of the park’s water scarcity is the Përroi i Thatë, a dry river whose valley runs through the entire territory of the park, from the northeast to the southwest. Although the river has carved out gorges and deep canyons, water is really only present after heavy rains or during periods of snow melting. This vast valley was formed during the earliest geological periods, but especially during the consecutive Ice Ages. This U-shaped valley around Bogë is a notable example of the power of glaciers to shape landscapes.

All the more or less plain areas up to an altitude of about 1000m above sea level have long been transformed into arable land, gardens, orchards or settlements. Meanwhile, natural masses like the old beech forests have dropped recently, and the few remaining beech forests are rapidly disappearing from unsustainable use. The wildest, most untouched parts of the region can only be found atop its inaccessible peaks and high mountain plateaus. These surfaces are where native pine forests (pinus heldreichii) can be found and these areas are the 'strongholds' of the Albanian flora endemisms.