There is no in-universe explanation. The filmmakers simply moved the lagoon a few miles (in the sequel) so that they could have a gate, which they also added, that leads out of the lagoon and to the outside ocean.
Before (Jurassic world)
After (Jurassic World: Fallen Kingdom)
Interestingly, the director Colin Trevorrow claims that this was an error by the VFX team (with the map seen on screen) and that the gate was supposed to lead to a series of unseen canals that would allow access to the ocean, allowing the lagoon to remain central on the island.
The lagoon is in the center of the island, connected to the ocean by a canal system. The digital maps in the film are incorrect, not a retcon. My fault for missing it, I had no idea the change was made until it was too late. Hope you guys can forgive it.
And other digital maps from the same design team (admittedly designed for the viral website rather than the film) have it back in its original place.