The first level is set at the bottom of the sea at night time. If the player swims down when a Blooper Nanny appears, they can access an area with many Blocks, Coins, and a block containing a 1-Up Mushroom. All 3 versions of Bloopers appear.
By allowing oneself to slide through the gap in the seafloor at the very beginning of the level, the player will find a secret area with a ? Block containing a Fire Flower. After the first Blooper, Mario can jump out of the water and scale the wall, finding another secret area with a Fire Flower.
After leaping onto the first moving platform, pushing against the a certain wooden block will reveal a Starman. When invincible, all ? Blocks along the way will hold more Starmen; if not, they will contain one coin. To reach the exit, Mario must enter a pipe when the Venus Fire Trap backs into the pipe.
This level features Boss Basses. If Mario approaches one, it will lunge at him with its mouth open, and if it eats Mario, he will instantly lose one life, even if he is equipped with an item. Even though the Boss Bass can be killed with a fireball, a new one will eventually come back. By stepping on a Koopa to the left of a Note Block and a huge formation of blocks, the player will reveal a P-Switch, allowing Coins to appear and the power-up in the Note Block to be grabbed more easily.
World 3-Fortress 1
This castle is a huge maze, with doors all leading to different places. The first, second, third, and fourth doors all lead to the same place: a pool of water with a ? Block concealing a power-up at the end, and two pipes that lead to the beginning of the level. The fifth leads to a secret ledge with a 1-Up in a block, the sixth to a ledge with the door to the Boom Boom battle, the seventh and eighth to the pool, but the last has a cache of coins that can be snagged by Raccoon Mario, or reached after hitting two hidden blocks on the left-hand side.
The level begins with two Goombas walking up a small slope. They can be easily dispatched by pressing and holding Down on the D-Pad while walking down the slope. Immediately afterward, a Piranha Plant inside a pipe is stationed. A ? Block right by yields either a Super Mushroom or a Fire Flower, depending on what the player currently is equipped with. A larger slope curves down nearby, with three Goombas walking up it.
Later in the level is a pipe extending from the top of the level downwards. The pipe contains a Venus Fire Trap. A P-Switch is revealed if one of the low blocks is hit from the bottom. When pressed, many Silver Coins appear near the area of the button. Ahead are two ? Blocks, one containing a Super Leaf. Shortly after, the Goal Panel is located.
This level introduces Jelectros, invincible jellyfish enemies, and Big Berthas, who look similar to Boss Basses, but simply shoot Baby Cheeps out of their maws. If Mario is equipped with a Frog Suit, he can go down a bubble-spewing pipe to gain access to three 1-Up Mushrooms.
This level is force scrolled, and constantly scrolls in a certain direction. A majority of the level requires Mario to jump from platform to platform to avoid falling.
On the stack of wood blocks Mario starts out on, the top one contains a powerup. In a later group of bricks, Mario can destroy them to reveal a 1-Up. After the first pipe, the player can grab a Koopa shell and release it at the top brick formation to grow a Magic Vine. It will lead to a series of cloud platforms, ending at a block that contains a P-Switch. There is also a hidden pink Note Block that takes Mario to a special Coin Heaven with a Jugem's Cloud at the end.
World 3-Fortress 2
This level introduces Stretches, platforms from which Boo heads protrude. Some Stretches have Boos on one side, while others have them on both. At the end of the level is a pipe leading to Boom Boom, the stage boss.
The Boss Bass is again present in this level. The water rises to higher levels, but Magic Vines are abundant, allowing Mario to reach safety. The solitary block later has a 1-Up, while the rest have either Magic Vines or Coins. The level later breaks into two paths, and rejoins by the end of the level. Also, if enough coins are collected in this level, a White Mushroom House with a P-Wing will appear.
The level features a pipe that leads to a secret room containing a Frog Suit.
After avoiding the many obstacles along the way, Mario will meet Wendy O. Koopa. She uses Candy Rings that bounce off walls as a weapon. After jumping on Wendy's head twice, she will start bouncing around the room, making her more difficult to jump on. After she is defeated, Mario is granted with the Magic Wand.
If the player has a Hammer in their inventory, they can break a rock to gain access to the canoe. The player can then control the canoe across the water to an island with two Mushroom Houses and two Spade Panels and a second island with a third Mushroom House.