Hi Safaa. Some dictionaries define this as having a rest or taking a break, which is what your sentence means.
The significant point to understand is that "come up for air" is a metaphor. When an animal holds its breath underwater it absolutely needs to come to the surface to get air to breathe. It may want to keep on fishing underwater or whatever, but after a certain amount of underwater activity in needs to get oxygen, and the only way to do it is to come to the surface, or it will die.
The same applies to a human underwater.