Once you've cleared the Suthorn Ruins dungeon, defeated the first boss, and cleared The Mysterious Rifts Main Quest, you'll be given a new Main Quest at Lueberry's House — Searching for Everyone. Tri will notice that there are two regions that are being swallowed up by Rifts and need saving — Jabul Waters and the Gerudo Desert.
While you can do these in any order, we'd recommend going to the Gerudo Desert first. This is because it's closer to the Suthorn region, being just west of the Suthorn Prairie — where you'll find a Heart Piece and the Side Quests Up a Wall and The Blocked Road.
The Gerudo Desert is also home to one of the best Echoes in the game, the Platboom. This is well worth getting as soon as you can, which will help you explore Hyrule even more. Jabul Waters is also home to a good traversal Echo in the Water Block, but the Platboom is useful even for Jabul.