Well, if I understood correctly, you're asking what's the difference in fishing in an area with bubbles. When fishing in a fishing spot with bubbles spewing out of the spot this mean the encounter pool will change. Usually rarer Pokemon will be found such as Dratini. Once you fish in a spot with bubbles the bubbles will disappear and if you run towards the spot the bubbles will vanish. In order to get those bubbles again you must leave the area then come back to respawn those bubbles.
Hope I've helped