When you are going through the water filled caves to find the Water Dragon, you will come to the middle cave area after jumping over the bars in the water. The cube will be sitting on the land that surrounds the cavern, on the far side across a bridge. Follow the walkway around to find it.
Item Recovered: Small Bomb Bag
At the bird statue for Floria Waterfall, look up above the statue and there will be a patch of vines there. Use the Clawshot to grapple up to it and you will find the cube hiding out there.
Item Recovered: Gold Rupee