Noki Bay predominantly consists of a large body of water and very tall cliffs, and can be accessed by Mario by collecting 20 or more shine sprites, standing on a mosaic located in Delfino Plaza, and looking towards the sun. Within the body of water that makes up most of Noki Bay, there are a number of submerged Noki homes which appear as platforms emerging out of the water, as well as three tall spiralling towers, covered in platforms, connected with wires, and each topped by an enormous sea shell. Towards one corner of the bay, a waterfall can be found, beneath which appear to be the ruins of an older set of Noki buildings. Near the waterfall there is also a shack owned by a Tanooki who rents his boats out to anyone willing to pay the price of 90,000 coins.
There are various paths along the cliffs to one side of the bay, while many others contain hidden tunnels and areas that can only be opened up by squirting water towards them. In one area, across the top of the cliffs, an entrance can be found to the tomb of an ancient Noki king. While progressing through the episodes of Noki Bay, Mario is aided and instructed by a Noki elder.
Episode 1: Uncork the Waterfall
In this episode the waterfall has been corked by the character Monty Mole. This has seemingly caused the whole bay to pollute, making the water dangerous to swim in. Mario must make his way across the water and up the cliffs to defeat Monty Mole and uncork the waterfall.
Episode 2: The Boss of Tricky Ruins
Unfortunately, despite Mario's efforts in the first episode, the bay remains polluted, and it is hypothesised this is due to Gooper Blooper having found his way to the top of the cliffs and sitting over the tomb of the ancient Noki king. Mario must climb the cliffs and defeat him.
Episode 3: Red Coins in a Bottle
The bay continues to remain polluted, however, the Noki elder believes he has figured out the cause of this pollution. To train Mario to fight it, he gives him a diving helmet, and shrinks him down so that the may enter a miniature bottle where he must collect 8 red coins without running out of breath.
Episode 4: Eely-Mouth's Dentist
In this episode, Mario manages to get beneath the waterfall into the ancient Noki ruins, where he finds the true source of the pollution, a giant eel called Eely-Mouth who is experiencing severe tooth decay. Without drowning, Mario must use FLUDD to clean Eely's mouth and stop the pollution.
Episode 5: Il Piantissimo's Surf Swim
This is a standard Il Piantissimo level, where Mario must race against Piantissimo and win.
Episode 6: The Shell's Secret
Using the wires and platforms adorning the Noki Bay towers, Mario must reach the top of one and enter the shell inside. Here he finds a warp zone which he must complete to gain the shine sprite.
Episode 7: Hold It, Shadow Mario!
A regular Shadow Mario Level, where Mario must chase after and defeat Shadow Mario using FLUDD.
Episode 8: The Red Coin Fish
In this episode Mario must dive down to the former home of Eely-Mouth where a fish made entirely of coins has begun swimming around. 8 of the coins that make up its body are the red coins Mario must collect to complete the episode.
Episode 9: A Golden Bird
Mario must traverse the ruins in this episode and upon reaching the top has to spray a golden bird, causing it to turn into a shine sprite.
Episode 10: Red Coins on the Half Shell
In this episode Mario must enter the warp zone from episode 6, and collect the 8 red coins within.