Forest fringed lakes, papyrus swamps, savannah plains and rolling highlands combined in a relatively small area make Akagera among the most scenic of savannah reserves. Akagera has exceptional levels of biodiversity, partly due to its position at the confluence of different vegetation zones. The extensive systems of freshwater lakes and associated papyrus swamps form the largest protected wetland in central Africa.
With Rwanda's high population density (currently the highest in continental sub-Saharan Africa at approximately 253 people/km2) biodiversity losses have been in the order of 90 – 95%. Akagera is the only protected savannah region in Rwanda and as such is the only refuge for savannah adapted plants and animals on a national scale. It complements the humid forests of Nyungwe National Park in the south of Rwanda and the afro-alpine habitats of Volcanoes National Park in the north.
Several species have been introduced into Akagera in recent decades. Until 1986 when six 'Masai' giraffe were introduced into Rwanda from Kenya, giraffe had never been recorded in the eastern savannas of Rwanda, despite bordering with Tanzania in an area where they were once profuse. Currently this population numbers over 100 individuals.
During 1957 five black rhino females and two males were brought in from Tanzania and subsequently thrived at Akagera. It is estimated that the population exceeded 50 in the late 1970s. However wide-scale poaching in the early 1980s wiped out the Akagera population almost entirely and the last confirmed sighting of a black rhino in Akagera was in 2007. The current management plan includes the re-introduction of black rhino and lion to the park once the western boundary fence is completed.
The current elephant population at Akagera was also introduced, but unlike giraffe and black rhino, elephants once occurred naturally in the park. The last sighting of the original population was in 1961 after which for unknown reasons they disappeared. In 1975 an attempt was made to move elephant from the Bugesera, an area of increasing human settlement south of Kigali, to Akagera, however the knowledge of elephant translocation was not what it is today and only young elephants could be moved whilst all the adults had to be exterminated. Among the group of 26 young elephant were three babies that needed hand-rearing and one youngster named Mutware "the Chief". Mutware became familiarized with humans and today he is well known amongst the surrounding communities. Unfortunately his notoriety is largely for his troublesome behaviour and his appreciation for the local banana beer "urwagwa”. Elephant numbers in Akagera are currently estimated at around 120 individuals.
An aerial census was completed in August 2010 with population estimates and survey parameters reported in the census summary. Akagera is home to many large plains game species as well as species restricted in range to the papyrus swamps. Species partial to the papyrus wetlands include the swamp-dwelling Sitatunga (Tragelaphus spekei) and the sought-after shoebill (Balaeniceps rex). Notable plains game include the savanna elephant (Loxodonta africana), buffalo (Syncerus caffer), topi (Damaliscus lunatus topi), zebra (Equus quagga boehmi), defassa waterbuck (Kobus ellipsiprymnus defassa) the secretive roan antelope (Hippotragus equinus) and the statuesque eland (Taurotragus oryx). Other antelope species listed in Akagera are duiker (Sylvicapra grimmia), oribi (Ourebia ourebi), bohor reedbuck (Redunca redunca), klipspringer (Oreotragus oreotragus), bushbuck (Tragelaphus scriptus) and impala (Aepyceros melampus).
Of the primate family, olive baboons (Papio anubis) and vervet monkeys (Chlorocebus pygerythus) are common, less so is the secretive blue monkey (Cercopithecus mitis) which was thought to have become extinct in Akagera until recently. Bushbabies or Galagos (Galago moholi and Otolemur crassicaudatus) are often seen on night drives.
Of the large predators only leopard (Panthera pardus) and hyaena (Crocuta crocuta) can still be found in the park. Although lion once occurred throughout Akagera, the population have been wiped out mostly through poisonings by cattle herders seeking to protect their livestock. A reduction in the prey-base due to heavy poaching would also have contributed to their demise. Smaller predators are still well represented with healthy populations of several mongoose species, viverrid species, serval (Leptailurus serval) and side-striped jackal (Canis adustus).
Due to its wide variety of habitats, Akagera is an important ornithological site with nearly 500 bird species. The rare and elusive shoebill shares the papyrus with other rarities such as the exquisite papyrus gonolek (Laniarius mufumbiri) and countless other water birds that inhabit the wetlands in large numbers.
A wetland bird survey was carried out in March 2011 by the Association for Conservation and Nature of Rwanda (ACNR), with assistance from park staff.