Sheikh Ahmed was the younger brother of Emirati President Sheikh Khalifa bin Zayed al-Nahayan, who is also the ruler of Abu Dhabi, although he was not in the immediate line of succession for the throne of the oil-rich emirate.
He has a home in the area where the ultra-light crashed near the Moroccan capital Rabat.
Dozens of divers from various countries, including Morocco, France, Spain, the UAE and the United States took part in the search.
A Moroccan source said at the weekend that the search had been complicated by recent heavy rain that had left water levels high and swamped surrounding areas.
Sheikh Ahmed's funeral will take place in Abu Dhabi on Wednesday, the state news agency WAM reported.