The lake is situated within the Western Rift of the geographic feature known as the Great Rift Valley formed by the tectonic East African Rift, and is confined by the mountainous walls of the valley. It is the largest rift lake in Africa and the second largest lake by volume in the world. It is the deepest lake in Africa and holds the greatest volume of fresh water. It extends for 676 km (420 mi) in a general north - south direction and averages 50 km (31 mi) in width. The lake covers 32,900 km² (12,700 sq mi), with a shoreline of 1,828 km (1,136 mi) and a mean depth of 570 m (1,870 ft) and a maximum depth of 1,470 m (4,820 ft) (in the northern basin) it holds an estimated 18,900 cubic kilometres (4,500 cu mi). It has an average surface temperature of 25 °C and a pH averaging 8.4.

The enormous depth and tropical location of the lake prevent 'turnover' of water masses, which means that much of the lower depths of the lake is so-called 'fossil water' and is anoxic (lacking oxygen). The catchment area of the lake covers 231,000 km², with two main rivers flowing into the lake, numerous smaller rivers and streams (due to the steep mountains that keep drainage areas small), and one major outflow, the Lukuga River, which empties into the Congo River drainage. ' The major river that flows into this lake, beginning 10.6 ka, is the Ruzizi River, entering the north of the lake from Lake Kivu. The Malagarasi River, which is Tanzania's second largest river, enters the east side of Lake Tanganyika. The Malagarasi is older than Lake Tanganyika and was formerly continuous with the Congo river. Lake Tanganyika is presently the second largest freshwater lake in the world by volume.

The lake holds at least 250 species of cichlid fish and 150 non - cichlid species, most of which live along the shoreline down to a depth of approximately 180 metres (590 ft). Many species of cichlids from Lake Tanganyika are popular fish among aquarium owners due to their bright colors. Recreating a Lake Tanganyika biotope to host those cichlids in a habitat similar to their natural environment is also popular in the aquarium hobby.

Lake Tanganyika is thus an important biological resource for the study of speciation in evolution. The largest biomass of fish, however, is in the pelagic zone (open waters) and is dominated by six species: two species of "Tanganyika sardine" and four species of predatory lates (related to, but not the same as, the Nile perch that has devastated Lake Victoria cichlids). Almost all (98%) of the Tanganyikan cichlid species are endemic to the lake and many, such as fish from the brightly coloured Tropheus genus, are prized within the aquarium trade. This kind of elevated endemism also occurs among the numerous invertebrates in the lake, most especially the molluscs (which possess forms similar to those of many marine molluscs), crabs, shrimps, copepods, jellyfishes, leeches, etc.

It is estimated that 25 – 40% of the protein in the diet of the approximately one million people living around the lake comes from lake fish. Currently, there are around 100,000 people directly involved in the fisheries operating from almost 800 sites. The lake is also vital to the estimated 10 million people living in the basin.

Lake Tanganyika fish can be found exported throughout East Africa. Commercial fishing began in the mid 1950s and has had an extremely heavy impact on the pelagic fish species; in 1995 the total catch was around 180,000 tonnes. Former industrial fisheries, which boomed in the 1980s, have subsequently collapsed.

There are two ferries which carry passengers and cargo along the eastern shore of the lake - the MV Liemba between Kigoma and Mpulungu and the MV Mwongozo, which runs between Kigoma and Bujumbura.

• The port town of Kigoma is the railhead for the railway from Dar es Salaam in Tanzania.
• The port town of Kalemie is the railhead for the D.R. Congo rail network.
• The port town of Mpulungu is a proposed railhead for Zambia.

The Lake was the scene of two famous battles during World War I.

With the aid of the Graf von Götzen (named after Count Gustav Adolf Graf von Götzen, the former governor of German East Africa), the Germans had complete control of the lake in the early stages of the war. The ship was used both to ferry cargo and personnel across the lake, and as a base from which to launch surprise attacks on Allied troops.

It therefore became essential for the Allied forces to gain control of the lake themselves. Under the command of Geoffrey Spicer - Simson the Royal Navy achieved the monumental task of bringing two armed motor boats Mimi and Toutou from England to the lake by rail, road and river to Kalemie on the western shore of Lake Tanganyika. The two boats waited until December 1915, and mounted a surprise attack on the Germans, with the capture of the gunboat Kingani. Another German vessel, the Hedwig, was sunk in February 1916, leaving the Götzen as the only German vessel remaining to control the lake.

As a result of their strengthened position on the lake, the Allies started advancing towards Kigoma by land, and the Belgians established an airbase on the western shore at Albertville. It was from there, in June 1916, that they launched a bombing raid on German positions in and around Kigoma. It is unclear whether or not the Götzen was hit (the Belgians claimed to have hit it but the Germans denied this), but German morale suffered and the ship was subsequently stripped of its gun since it was needed elsewhere.

The war on the lake had reached a stalemate by this stage, with both sides refusing to mount attacks. However, the war on land was progressing, largely to the advantage of the Allies, who cut off the railway link in July 1916 and threatened to isolate Kigoma completely. This led the German commander, Gustav Zimmer, to abandon the town and head south. In order to avoid his prize ship falling into Allied hands, Zimmer scuttled the vessel on July 26, 1916. The vessel was later resurrected and renamed as the MV Liemba.

In 1965 Argentinian revolutionary Che Guevara used the western shores of Lake Tanganyika as a training camp for guerrilla forces in the Congo. From his camp, Che and his forces attempted to overthrow the government, but ended up pulling out in less than a year since the National Security Agency (NSA) had been monitoring him the entire time and aided government forces in ambushing his guerrillas.

In 1992 Lake Tanganyika featured in the documentary series Pole to Pole. The BBC documentarian Michael Palin stayed on board the MV Liemba and traveled across the lake.

Since 2004 the lake has been the focus of a massive Water and Nature Initiative by the IUCN. The project is scheduled to take five years at a total cost of US$ 27 million. The initiative is attempting to monitor the resources and state of the lake, set common criteria for acceptable level of sediments, pollution, and water quality in general, and design and establish a lake basin management authority.