In 1990 Sudan had only one operational deep-water harbor, Port Sudan, situated on an inlet of the Red Sea. The port had been built from scratch, beginning in 1905, to complement the railroad line from Khartoum to the Red Sea by serving as the entry and exit point for the foreign trade the rail line was to carry. It operated as a department of SRC until 1974 when it was transferred to the Sea Ports Corporation, a newly established public enterprise set up to manage Sudan's marine ports. Facilities at the port eventually included fifteen cargo berths, sheds, warehouses, and storage tanks for edible oils, molasses, and petroleum products. Equipment included quay, mobile, and other cranes, and some forklift trucks, but much of the handling of cargo was manual. There were also a number of tugboats, which were used to berth ships in the narrow inlet.

During the early 1970s, port traffic averaged about 3 million tons a year, compared with an overall capacity of about 3.8 million tons. Exports were somewhat more than 1 million tons and imports about 2 million tons about half of the latter was petroleum and petroleum products. By the mid-1970s, stepped up economic development had raised traffic to capacity levels. In 1985, however, largely as a result of the civil war, exports were down to 663 thousand tons (down 51 percent from the previous year) and imports were 2.3 million tons (down 25 percent from the previous year). Physical expansion of the harbor and adjacent areas was generally precluded by natural features and the proximity of the city of Port Sudan. However, surveys showed that use could be increased considerably by modernization and improvement of existing facilities and the addition of further cargo-handling equipment. In 1978, with the assistance of a loan from the IDA, work began on adding deep-water berths and providing roll-on-roll-off container facilities. A loan to purchase equipment was made by a West Germany body. The first phase was completed in 1982, and the second phase began in 1983, aided by a US$25-million World Bank credit. One of the major improvements has been to make the port more readily usable by road vehicles. Developed almost entirely as a rail-serviced facility, the port had large areas of interlacing railroad tracks that were mostly not flush with surrounding surfaces, thereby greatly restricting vehicular movement. Many of these tracks have been removed and new access roads constructed. Much of the cleared area has become available for additional storage facilities.

In the early 1980s, the Nimeiri government announced a plan to construct a new deep-water port at Sawakin, about twenty kilometers south of Port Sudan. Construction of a new port had long been under consideration in response to the projected growth of port traffic in the latter part of the twentieth century. A detailed study for the proposed port was made by a West German firm in the mid-1970s, and plans were drawn up for three general cargo berths, including roll-on-roll-off container facilities, and an oil terminal. Major funding for the port, known as Sawakin, was offered i81e in 1985 by West Germany's development agency Kreditanstalt für Wiederaufbau and the DFC. After the Nimeiri government repeatedly postponed work on the port, the German government allocated the funds instead for purchase of agricultural inputs. Once work resumed, however, Sawakin port opened in January 1991, and was capable of handling an estimated 1.5 million tons of cargo a year.

A national merchant marine, Sudan Shipping Line, was established in 1962 as a joint venture between the government and Yugoslavia. In 1967 it became wholly government owned. From the initial two Yugoslav-built cargo vessels, the line had grown by the mid-1970s to seven ships, totaling about 52,340 deadweight tons. During 1979 and early 1980, eight more ships were added, including six built in Yugoslavia and two in Denmark. In 1990 the merchant marine consisted of ten ships of 122,200 deadweight tons. The Yugoslav vessels were all multipurpose and included container transport features. The Danish ships were equipped with roll-on-roll-off facilities. Sailings, which had been mainly between Red Sea ports and northern Europe, were expanded in the late 1980s to several Mediterranean ports.

Data as of June 1991