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Aqueduct is an structure (usually made by concrete) that carries the water but level of water passage is not sticking to the ground. on the other hand an aqueduct is a bridge with a canal on top of it. aqueducts usually used in cross point of canals with other structures (such as roads, bridges, other canals and etc.). first aqueducts was made by Romans to transport water from highlands to their cities.
But canals usually is made on natural ground by digging land and lining the walls and bed by Reinforced concrete or the other materials for protecting surfaces from leakage and abrasion.