At approximately 277.5 km2 (107.1 sq mi), the park encompasses the country's sections of the Great and Small Prespa Lake.

It is considerably characterised by high mountains, narrow islands, vast freshwater wetlands, salt marshes, meadows, reed beds and dense forests.

During classical antiquity, the trade route of Via Egnatia passed nearby the region as it was inhabited by several Illyrian and Ancient Greek tribes as well as Romans and later by Byzantines.

[13][14] The Prespa National Park is strategically located in the southeastern region of Albania, bordering North Macedonia to the northeast and Greece to the southeast.

[15] The Great Prespa Lake is shared between Albania in the west, North Macedonia in the northeast and Greece to the southeast.

[17] The lakes are surrounded by high mountains including Mali i Thatë in Albania and Galičica in North Macedonia.

[19] The reed beds occur along stream and river margins, where the flow is slower but are found most extensively on the lakes.

[19] They have great conservation value as they provide a good breeding and roosting site for a variety birds and other species.

[19] The pelagic zone covers the deep, mainly naturally, non-vegetated parts of the lakes, where emergent plants cannot grow.

The riverine zone encompasses some of the largest and most diverse stream and channel systems in the region, including extensive wetlands, floodplains and mangroves that support vast numbers of water birds and other aquatic and marine species.

[19] As we climb from the hills to the mountainous areas, the oak forests change into beech spreading in the slopes of Mali i Thatë.

[19] Areas of grassland with alpine and sub-alpine meadows and pastures dominate much of the crests and eastern slopes of Mali i Thatë and provide an important habitat for the diverse wildlife that lives in abundance here.

The landscapes of the park have evolved, together with the floral and faunal resources, as part of the evolution of the Prespa Lake Basin some million years ago.

[20] Due to the density of vegetation that makes some areas rather inaccessible to people, much of the preserved forests, bushes and grasses have remained relatively undisturbed by human intervention that in turn offers important shelter for animals.

The white and dalmatian pelican, which is one of the largest bird species in the world, spend the summer season in the lakes of the park associated with the undisturbed wetlands, freshwater marshes and permanent streams.