Like water to a fish, this thing is not entirely imperceptible but it is rarely noted, if at all.
simile or metaphor might work best. "just part of the scenery", "as familiar as the furniture". Or you could say that something "disappeared into the background".
Though I'm unable to access a single word which includes the cause of the imperceptions, single words which are suggestive of your question:
Medium, i.e., ‘these organisms were growing in their natural medium’; Ambient: completely enveloping; Elemental, in the sense of being so fundamental as to be imperceptible; Milieu: the surrounding environment or setting.
You can consider overfamiliar.
- common or repeated to the point of being unnoticed or annoying
- (Used with “with”) so acquainted with something, that one doesn't notice it, or is annoyed by it
As you can see from the definition, an overfamiliar thing/person can be either unnoticed or annoying. But the latter sense seems like more common.
Scientifically, this phenomenon is related with subconscious mind and even inattentional blindness.
For example, breathing is controlled by subconscious most of the time unless you pay attention to it.
Inattentional blindness suggests that even the most common things go unnoticed if you do not pay close attention to them.
Fish/water example is a bit controversial though. For example, There is a question circling around the internet: "Does a fish know it is wet?". It can also be asked as "Does a fish know it is in water?". This is related to the intelligence level of the fish. They do not think concepts as human do. Their perceptions and memory systems are different. They might just know that they survive in the environment that they are in.
Though, there are also intelligent species that live in the water. For example, dolphins. They are mammals and they can stay out of water for a while. They also rise to the surface to breathe. They might be perceiving different environments and they might know the difference between wet and dry.