From Bulbapedia, the community-driven Pokémon encyclopedia.
The Sea Crown (Japanese: 海の王冠) is an item of great value that resides in Samiya. Its foundation is a large stone, shaped similarly to a layered cake. It has many light-blue crystals sticking out of it that can be removed. It has the power to bestow the traits of Water-type Pokémon to people who are near it, giving them the ability to breathe water and swim through it rapidly.
The Sea Crown is a mysterious piece of technology that appears to have multiple functions: It is a sort of "Engine" that propels the temple through the underwater depths, it emits a Containment Bubble that refracts light from the outside (rendering it invisible unless exposed to red moonlight) and maintains a breathable atmosphere on the inside, and it controls and stabilizes the limitless amounts of incoming water that flow throughout the structure's aqueduct system.
Phantom, by removing one of the Crystals which acts as its power source, compromised the Containment Bubble which allowed the surrounding ocean to flow into the temple at an uncontrollable rate. It soon stopped moving, started to lose buoyancy, and began sinking. Fortunately with the help of Jackie, Ash, and May, the jewels were returned to the Sea Crown, effectively restoring the Containment Bubble and saving the Sea Temple from irreversible destruction.
It also has some mystical power, as apparently, whoever repairs the Sea Crown (in this case, Ash) is surrounded by a yellow aura, allowing him to swiftly fly through the water to rescue Manaphy.