From my experience, in each area, there is one fishing spot that is always bubbling the first time you see it; the others never bubble at all. So, when you go to this spot, be very careful; running/using a Ride Pokemon to it will make the bubbling go away, and it will become a noal fishing spot. Once you successfully throw your line into it, you have one chance, as running away from, defeating, or catching the Pokemon that comes out, obtaining an item, or getting nothing all make it go away.
1. There's one fishing spot that always bubbles in each area
2. Don't run to it
3. You have one chance to get what you're looking for, for if you don't, it goes away and you have to try again.
Hope I could help!