The Rift Valley is at its most impressive at Lake Manyara, with the escarpment dropping a dramatic 500 m (1 640 feet) down to the lakeshore. Water in Lake Manyara is trapped and subjected to intense evaporation, which has led to salt accumulation and the appearance of distinctive deposits at the water’s edge. In spite of the water's salinity, the lake houses large pods of hippo and the high concentration of algae attracts an astounding array of water birds. Groves of tall, ghostly fever trees grow on the banks of the lake during the dry season, dying off as the level of the lake rises and the tree roots become waterlogged. New forests spring up in the next dry season, continuing the perpetual cycle.

Permanent pools on the fringes of the marshes are irresistible wallowing sites for elephant, buffalo and warthog. This waterlogged habitat is also home to the specially adapted reedbuck and waterbuck, and several rarely encountered species, such as the serval and marsh mongoose. An abundance of frogs that breed in the marshes attracts a range of snakes, including the African rock python. During the dry seasons, the waters of Lake Manyara recede and stretches of exposed land are covered with tender grasses attracting many grazing herbivores, such as wildebeest, zebra, buffalo and warthog.

While most large mammals can be found in the woodlands, extensive shrubby areas provide a protected habitat for the Kirk’s dik-dik. Tall termite mounds are often occupied by dwarf and banded mongoose, as well as monitor lizard. Birds are plentiful, due to the abundance of insects, nectar and seedpods. Nurtured by a permanent supply of groundwater, a tall, evergreen forest thrives in the park's northern region. Most large mammals avoid the boggy conditions of the forest, but elephant and buffalo occasionally feed here and bushbuck are commonly encountered. Troops of blue monkey and olive baboon forage through the tree canopies.