Lake Bogoria, being alkaline, supports the growth of blue-green algae, which serves as a primary food source for flamingoes. The lake can host an impressive number of these birds, reaching up to two million at certain times. Raptors like tawny eagles prey on the flamingoes, contributing to the rich avian diversity with a recorded total of 135 bird species. Among them are the little grebe, pratincole, swift, little bee-eater, cape wigeon, yellow-billed stork, African spoonbill, augur buzzard, gabar goshawk, water dikkop, great tit, starling, hornbill, and crombec.

Within the reserve, there is a herd of the relatively uncommon Greater Kudu, adding to the variety of large mammals that include buffalo, zebra, cheetah, baboon, warthog, caracal, spotted hyena, impala, and dik-dik.

The Waseges River traverses areas of intense coffee cultivation marked by the heavy use of chemical fertilizers and pesticides, posing a potential threat of pollution to the lake. The hot springs along the western lakeshore attract numerous visitors but also contribute to pollution through solid wastes. Siltation stands as another concern, posing a threat to the overall biodiversity of the area.