Basically underwater caves with air in them only have air in the parts that are above the water table. Caves are complex 3D structures, and while access might be restricted to underwater entry only, plenty of the cave complex may be above the water table. Small cracks and porous rock let air in from the surface.
In places with tides wierd things can happen that may pump air into unexpected places below the water table but you won’t have air too far down.
Some other caves that are only accessible with diving gear may actually be above the water table for the most part, but have parts that are mostly filled by flowing water that collects in the low parts of the caves.
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