The flotilla included four cargo vessels and a Turkish passenger ferry carrying some 600 people.
The Istanbul-based foundation for Human Rights and Freedom and Humanitarian Relief helped to organise the convoy.
Human rights workers and lawmakers from several European countries are reported to be among those on board.
The flotilla set sail for Gaza despite a ban from Cyprus, which said it would not let the ships sail from its ports.
Palestinian fishermen in Gaza had already prepared their boats ahead of the expected arrival of the flotilla.
The cargo included cement, water purification kits, pre-fabricated homes and medical equipment.
The organisers deny they had weapons on board.