You get this by unlocking (with coins) the various ruins around the islands and sending your dragons in the explore. You'll need to level up the specific dragons before sending them off and there's a time you have to wait before they return.
Even with all this, there's no guarantee they'll return with a Seal Shard each trip as it seems to just be a chance % each time. You can maximize your chances by sending them often as well as unlocking more ruins to explore.
I got this after unlocking the first ruin, Mystic Cave, where I randomly found 2 shards after several attempts as well as unlocking the Ghost Ship, where I got my third shard and the achievement unlocked.
Also of note, if you get this on one platform and the other one doesn't unlock, try closing the game entirely and open it again. This popped for me first on WP (See solution below), but Windows 8 didn't pop until I closed the app and re-opened it.
Lastly, you'll likely get this other achievement on your way: