Defeat the enemies along the way then restore the broken part of the aqueduct using the amulet. Once repaired, continue to the end of the aqueduct to reach the Gorgon Eye chest and two red chests.
Jump to the lower ground and take out all enemies to unblock the path. You'll find a decayed chest along the way. Restore it and follow the corridor. Turn to the right before reaching the health and magic chests to find another decayed chest.
Cistern Decayed Chests 1 and 2
Defeat the ogre and the parasites but before restoring the wooden bridge, head to the right to find another decayed chest. Jump on the lower ground below and you'll find two red chests again inside the house. Proceed further to the right to find yet another decayed chest.
Cistern Decayed Chests 3 and 4
Return to the upper ledge and restore the wooden bridge. Cross it and continue past the chasm and follow the path until you reach the large machine you encountered before. Restore it using the amulet but not completely; you should restore it enough to clear the large piece of debris along the crank's path. Once it is lifted, pull the crank all the way to the end then use the amulet again to decay, for the large piece to block the crank and prevent the wheel from moving. Before stepping on the green platform, collect the red orbs from the chests behind the watermill.
While on standing on the green platform, use the amulet to fully restore the watermill. Jump to the broken part of the aqueduct and restore it for the water to flow freely in the watermill.