More than 90 percent of the country consists of desert areas: In the west, the Libyan Desert, a part of the Sahara Desert which is also known as the Western Desert. The Libyan Desert includes a vast sandy expanse called the Great Sand Sea. Located here are several depressions with elevations below sea level, including the Qattara Depression, which has an area of about 18,000 sq km (about 7000 sq m) and reaches a depth of 133 m (436 ft) below sea level, the lowest point in Africa. Also found here are the oases of Siwa, Kharga, Baharia and Dakhla.

In the east the Arabian Desert, also called the Eastern Desert (which borders the Red Sea and the Gulf of Suez). Much of the Arabian Desert occupies a plateau that rises gradually east from the Nile Valley to elevations of about 600 m (about 2000 ft) in the east and is broken along the Red Sea coast by jagged peaks as high as about 2100 m (about 7000 ft) above sea level., In the extreme south, along the border with Sudan, is the Nubian Desert, an extensive region of dunes and sandy plains.

The Sinai Peninsula consists of sandy desert in the north and rugged mountains in the south, with summits looming more than about 2100 m (about 7000 ft) above the Red Sea. Mount Catherine (Jabal Katrìnah - 2637 m/8652 ft), the highest elevation in Egypt, is in the Sinai Peninsula, as is Mount Sinai (Jabal Mosa), where, according to the Old Testament, Moses received the Ten Commandments.

The Nile enters Egypt from the Sudan and flows north for about 1545 km (about 960 m) to the Mediterranean Sea. For its entire length, from the southern border to Cairo, the Nile flows through a narrow valley lined by cliffs. Lake Nasser, the world's largest man-made reservoir and formed by the Aswan high dam, extends south across the Sudan border. The lake is about 480 km (about 300 m) long and is about 16 km (10 m) across at its widest point. About two-thirds of the lake lies in Egypt.

South of a point near the town of Idfu, the Nile Valley is rarely more than 3 km (2 m) wide. From Idfu to Cairo, the valley is about 23 km (about 14 m) in width, with most of the arable portion on the western side. In the vicinity of Cairo the valley merges with the delta, a fan-shaped plain, the perimeter of which occupies about 250 km (about 155 m) of the Mediterranean coastline. Silt deposited by the Rosetta (Rashid), Damietta (Dumyat), and other distributaries has made the delta the most fertile region in the country. However, the Aswan High Dam has reduced the flow of the Nile, causing the salty waters of the Mediterranean to erode land along the coast near the Nile.

A series of four shallow, brackish lakes extends along the seaward extremity of the delta. Another larger lake, Birkat Qarun, is situated inland in the desert north of the town of Al Fayoum., Geographically and traditionally, the Nile Valley is divided into two regions, Lower Egypt and Upper Egypt, the former consisting of the delta area and the latter comprising the valley south of Cairo., Although Egypt has about 2450 km (about 1520 m) of coastline, two-thirds of which are on the Red Sea, indentations suitable as harbours are confined to the delta. The Isthmus of Suez, which connects the Sinai Peninsula with the African mainland, is traversed from the Mediterranean to the Gulf of Suez by the Suez Canal.