Being a superhero has certain difficulties because some of Barnacle Boy's biological systems underwent changes during his transformation and are compromised by his underwater living situation.
Deep-diving can result in mechanical distortion and tissue compression, especially in gas-filled spaces in the body, such as the middle ear cavity, air sinuses in the head, and the lungs.
He would lose too much water through osmosis because he would constantly be in a hypertonic solution (the ocean). This would be a problem because he could shrivel up and die.
Undersea temperatures can get very low and any animal without sufficient insulation or metabolic processes would freeze to death.