After the confluence with the Lumpungu River, the Malagarasi enters Tanzania, makes a circle and empties into the eastern side of Lake Tanganyika about 25 miles (40 km) south of Kigoma, near Ilagala.

[1] About 80 kilometres (50 mi) from the mouth, the river flows through the Moyowosi swamplands, an area of "extensive swamps and floodplains" and a "marshy labyrinth".

[1] With a basin area of 130,000 square kilometres (50,000 sq mi), the Malagarasi has the largest watershed of all of the rivers flowing into Lake Tanganyika.

[14] According to ecologist Rosemary Lowe-McConnell, "the Malagarasi and the Rungwa River are assumed to be relict headwaters of the extended pre-rift Zaire system".

Lake Tanganyika has since said to have "undergone both transgression and regression, depositing new sediments, altering the delta, and changing the course of the river".

[19] The tree species in the Malagarasi basin include Albizia gummifera, Bridelia micrantha, Cyperus papyrus, Diospyros mespiliformis, Ficus sycomorus, Ficus verruculosa, Isoberlinia spp., Khaya senegalensis, Parkia filicoidea, Phoenix reclinata, Syzygium cordatum, and Syzygium owariense.

[5] Giant freshwater Mbu pufferfish, however, occur in both the Central and Upper Zaire Basin and the Malagarasi River.

[22] The Malagarasi-Muyovozi Wetlands lie in the middle of the basin, at 1200 meters elevation at the confluence of the Malagarasi with the Gombe, Muyovozi, Ugalla, and other tributary rivers.

Seasonally-flooded grasslands on the surrounding floodplain vary seasonally and with annual rainfall, and can cover up to 1.5 million hectares (3.7×10^6 acres).

The floodplain supports extensive grasslands, dominated by the grasses Echinochloa haploclada, Themeda triandra, Setaria spp., Andropogon spp., Eragrostis spp., Digitaria spp., and Sporobolus spp.