Burundi has 14 protected areas divided into 4 categories, namely National Parks, Natural Reserves, Natural Monuments and Protected Landscapes totaling approximately 154,650 ha, or 5.5% of the country's total. These protected areas contain a lot of ecosystems. However, considering the current areas of large ecosystems, it appears that several of them are very poorly represented in the system of protected areas, including marshes, Lake Tanganyika, rivers and open forests (Nzigidahera, 2000). Regarding swamps, Burundi has areas that are still intact up to 40,000 ha.
The unprotected marshes occupy about 32464 ha while the protected ones occupy about 3799 ha and are located in the Rusizi Nature Reserve, the Ruvubu National Park and around the Lake Rwihinda Managed Reserve. Of the four major rivers, namely the Rusizi, Ruvubu, Akanyaru and Malagarazi rivers, only the first 2 are protected in their lower reaches.

The Malagarazi swamp complex is not represented in the national system of protected areas. The dynamics of this hydrological system have not been studied as well, but its importance in storing, regulating water flow, and as a reserve of land usable during the dry season is obvious. The Malagarazi swamp complex is also very rich in biodiversity, both fauna and flora.

The need to protect the Malagarazi swamp complex has long been recognized in Burundi. Indeed, the National Strategy and Action Plan for Capacity Building in Biological Diversity stipulates that a substantial section of this complex, the Lower Malagarazi - Lower Rumpungwe complex, more exactly 5 to 8 km from the Malagarazi Valley before entering Tanzania, and 3 to 5 km from that of Rumpungu before its confluence with the main river, be granted a special protection status.

Efforts to protect the Malagarazi swamp complex by Burundi would complement those of Tanzania, where the upper Malagarazi-Muyovozi system has already enjoyed RAMSAR site status since 2000. The protection of this locality would therefore aim to maintain this cross-border ecosystem, which is a refuge for the fauna and flora destroyed elsewhere in the depression or even throughout Burundi.