Egypt, Ethiopia and Sudan have signed a declaration of principles on Monday, in a critical step towards resolving a four-year dispute over Nile water sharing arrangements among Basin countries.
The details of the agreement are expected to be announced later.
"For thousands of years, the Nile water has been flowing with God's order," El-Sisi told hundreds of Nile Basin delegates who gathered in the Sudanese capital of Khartoum for the announcement of a deal.
"We could cooperate and accomplish great things or disagree and hurt each other…we have chosen to cooperate," El-Sisi told the audience to strong applause.
Speaking ahead of Egypt's president, Ethiopia's Prime Minister Hailemariam Desalegan stressed that the Renaissance dam his country has been building to generate electricity for economic development projects would not cause any harm to the Egyptian people.
"Egypt and the rest of the Nile Basin countries are "one family," Desalegan said.
"We covered a big step forward by reaching the declaration of principles," Desalegan said.
Ethiopia chose to take the "collaborative path" on the issue of distribution of the Nile water, he added.
Egypt's President El-Sisi had arrived in Khartoum on Monday for eleventh hour talks with Sudan and Ethiopia as the three countries prepare to sign a tripartite agreement on Addis Ababa's giant Nile dam project.
The three countries are also expected to agree on an international firm to conduct studies on the impact of the construction of the dam on flow levels.
On Tuesday, El-Sisi will head to Addis Ababa to conduct bi-lateral talks with Ethiopian authorities.
The Egyptian president is expected to ask the Ethiopian parliament to issue a formal recognition of Egypt's rights to its share in the Nile water in excgange for Cairo backing Addis Ababa's economic development project.
Egyptian officials had said any potential deal on sharing the Nile waters and operating Ethiopia's contested dam, would be binding on the three signatory states.
Egyptian Irrigation Minister Hossam Moghazy stressed any agreement would oblige Ethiopia to amend the dam's specifications if consultancy studies on the hydroelectric project if the project proves it could harm downstream countries.
For several years, Egypt has raised fears Ethiopia's under-construction $4.2 billion Grand Renaissance Dam would negatively affect its Nile water share.
The Ethiopian 6,000 megawatt dam, set to be Africa's largest, is expected to be fully completed by 2017. Ethiopia has finished constructing at least 40 percent of the dam.