I would suggest bringing both water shoes (i.e. for when you are in the Natural Pool) and sneakers (i.e. for driving to/getting down all of the stairs to the Natural Pool) with you. You may want to bring one towel to share amongst the three of you (you will dry off in the sun fairly quickly anyway) and 3 pairs of water shoes in your backpack (fewer towels = more space in backpack).
P.S. Would love to hear some feedback on the Aruba Off-Road tour (i.e. whether it is worth it or not).