They wre dug in repeating sqare paterns but i didn't find how they dug them.
Most likely with hoes: The earliest evidence of water control in ancient Egypt is the famous historical relief of the mace head of Scorpion King which dates to around 3,100 BC. It depicts one of the last predynastic kings, holding a hoe and ceremoniously cutting a ditch in a grid network. Besides attesting to the importance of these waterworks and the great ceremony attached to them, this picture confirms that Egyptians began practicing some form of water management for agriculture about 5,000 years ago. Source: http://www.waterhistory.org/histories/nile/t1.html