These Reefs are found all around the seas of Concordia, so you have some work ahead of you before you can find them all. Note as well that some of the Hidden Reefs are only unlocked later on in the game,

After completing the first main island, Willma will ask for your help in saving both of her kids, Billdit and Maykit who went to separate places. Before making your choice, there will be a notification indicating this choice has more weight than you may think; here's how your choice affects the game.