It was possible to travel from the Victoria lake to the Mediterranean sea (and vise versa). At the same time there were hydrological connections between the Chad basin and the great Lakes and between the great lakes and the Congo basin. And from the Chad area to the Niger area.
From the Jos plateau (cradle of Nok culture) it is possible to reach Lake Chad via the Komadugu River.
It is also possible to travel to Cameroon and near Chad Lake, via the Benue River, which is a tributary of the Niger. From the Benue River, it is possible to reach the Logone which flows north towards the lake in Chad.
From Chad Lake it is possible to take the Chari River towards the Congo River. A recent study was published about the Congo basin, describing it as a massive swamp 4,000 years ago.
The rivers of Dja and Kadei are born in Cameroon and head south-east to throw themselves into the Sangha river, which is a tributary of the Congo River.
The Uele River has its source close to the White Nile and Lake Albert.
My points are:
1) That people could move at that time on very large distance via boats.
2) That there were already beautiful civilizations in the Niger basin at that time.
Sub-Saharan Africa was marked by the Bantu expansion some time later, with Niger-Congo-speaking peoples expanding out of West Africa between about 3,000 BCE to 500 CE. This at best just takes Bantu speakers to the very peripheries of the Egyptian sphere, the modern slave trade and maritime trade with East Africa are probably likelier causes. https://en.wikipedia.org/wiki/Bantu_expansion