The Red Sea gradually receded over the centuries, its coastline slowly moving farther and farther southward away from Lake Timsah and the Great Bitter Lake to its present coastline today. Coupled with persistent accumulations of Nile silt, maintenance and repair of Ptolemy's canal became increasingly cumbersome over each passing century. 

Two hundred years after the construction of Ptolemy's canal, Cleopatra seems to have had no west-east waterway passage, because the Pelusiac branch of the Nile River, which had fed Ptolemy's west-east canal, had by that time dwindled, having choked up with silt.
Receding Red Sea and the dwindling Nile
Alternatives
Connections between the shores
Repair by Tāriqu l-Ḥākim