Despite the limited rainfall, Egypt boasts a diverse range of natural vegetation. While the Western Desert is devoid of plant life, areas with water support the growth of perennials, grasses, and a rich variety of plants along the coastal strip in spring. The Eastern Desert receives sparse rainfall but still sustains a varied vegetation including tamarisk, acacia, markh, thorny shrubs, small succulents, and aromatic herbs. The wadis of the Red Sea Hills, Sinai, and the ʿIlbah Mountains showcase even more striking growth.

The Nile, along with irrigation canals and ditches, provides a habitat for numerous water plants. The lotus of antiquity can be found in drainage channels in the delta. Grasses are abundant, with over 100 different types, including bamboo and esparto. Robust perennial reeds such as the Spanish reed and common reed are widely distributed in Lower Egypt, while the papyrus, once cultivated, is now limited to botanical gardens.

The date palm, both cultivated and subspontaneous, thrives throughout the delta, Nile valley, and oases. The doum palm is particularly associated with Upper Egypt and the oases. Native trees are scarce, with the Phoenician juniper being the only native conifer. Acacia, eucalyptus, and sycamore are widely distributed, while imported species like jacaranda, royal poinciana, and lebbek have become characteristic features of the Egyptian landscape.

In terms of domestic animals, buffalo, camels, donkeys, sheep, and goats are common, with goats being particularly noticeable in the countryside. However, animals depicted in ancient Egyptian friezes such as hippopotamuses, giraffes, and ostriches no longer exist in Egypt. Crocodiles are only found south of the Aswān High Dam. The largest wild animal is the aoudad, surviving in the southern parts of the Western Desert. Other desert animals include the Dorcas gazelle, fennec fox, Nubian ibex, Egyptian hare, and two types of jerboa. The Egyptian jackal still exists, and the hyrax can be found in the Sinai mountains. Carnivorous mammals include the Caffre cat and the ichneumon. Various lizard species, including the large monitor, can be found, as well as poisonous snakes such as vipers and the Egyptian cobra. Scorpions are common in desert regions, and there are numerous species of rodents. Insects, including locusts, are also abundant.

Egypt is home to a rich birdlife, with over 200 migrating bird species passing through during spring and autumn migrations. Additionally, there are more than 150 resident bird species. The hooded crow is a familiar resident, while the black kite is characteristic along the Nile valley and in Al-Fayyūm. Birds of prey include the lanner falcon and kestrel, while lammergeiers and golden eagles inhabit the Eastern Desert and Sinai Peninsula. The sacred ibis is no longer found, but the great white egret, cattle egret, and hoopoe can be seen in the Nile valley and Al-Fayyūm. The desert is home to around 24 distinct species of resident birds.

The Nile is home to approximately 190 varieties of fish, with the most common being bulṭī and Nile perch. The lakes on the delta coast mainly contain gray mullet. Lake Qārūn in Al-Fayyūm governorate has been stocked with būrī, while Lake Nasser is home to bulṭī, which grow to large sizes in its waters.