The first phase requires six hits, and Acro constantly bobs up and down randomly in the water. One advantage of using bomb is that the hitbox of the bomb lingers for about a second after it hits something, so Acro's vulnerability can be anticipated by "buffering" the bomb throws. My visual cue for when he first becomes vulnerable is to float to the top of the screen and throw a bomb when his HP becomes 2/3 full.
The better pattern for the second phase is when he moves left and right and shoots torpedoes. One advantage of using bomb in this fight is that it can hit Acro when he's below the screen. My setup for getting the first hit is to hold up the whole transition between the first and second phase (Kirby should be hugging the top of the screen for some portion of it) and throw a bomb when the health meter is 1/3 full.
The other pattern involves Acro going for a dive and shooting upwards. Before he shoots past you, five hits (out of six needed) are possible, so after he reappears at the bomb, I start spamming bombs, hoping that he spawns near where I'm throwing.
After the second phase, remove your powerup by taking it out and grabbing the shard, causing it to shatter.