The layout of the beach in the Sirena Beach stage strongly resembles the GameCube controller. One of the pools represents the grey analog stick, while the others are the A, B, X and Y buttons. The flame at the center is the START button, and the chairs are where the Nintendo GameCube logo would be. The two cabana huts are positioned to form the D-pad and C analog stick.

Within one of the bell towers in Delfino Plaza is a Rocket Nozzle box. The box is inaccessible without the use of a cheat device, and is only visible through the use of camera glitches.

Each location on Isle Delfino contains an Italian word. This is likely in reference to Mario's nationality.
• Delfino Plaza - Dolphin Plaza
• Bianco Hills - White Hills
• Ricco Harbour - Rich Harbour
• Gelato Beach - Ice Cream Beach
• Pianta Village - Plant Village
• Noki Bay - Shell Bay
• Pinna Park - Fin Park
• Sirena Beach - Siren Beach
• Corona Mountain - Crown Mountain

In a 2002 staff interview with Nintendo Dream, director Yoshiaki Koizumi revealed that FLUDD was inspired by his memories of playing with water guns as a kid, an image that he recalled upon first using the analog L & R triggers on the GameCube's controller. Series creator Shigeru Miyamoto further explained that the concept behind FLUDD was controversial among Nintendo's staff due to Mario not being widely associated with these kinds of tools, though Luigi's use of the Poltergust in Luigi's Mansion ultimately served as a precedent in the concept's favor.

In the same interview, Takashi Tezuka stated that Nintendo went to great lengths to keep FLUDD from resembling a firearm, both due to Koizumi finding a water gun "too simple" and due to concerns that guns (or anything that audiences may interpret as such) would be inappropriate for the franchise's public image. The "weird backpack thing" that FLUDD ultimately ended up as addressed both concerns at once, with Koizumi likening it to firefighting equipment and "a [plastic] bottle water rocket toy."

In a 2002 developer interview archived by the now-defunct blog GSLA, director Yoshiaki Koizumi revealed that the game's staff originally came up with ten different nozzles for FLUDD, devising new ones for each possible situation Mario might encounter. However, this was reduced to three to avoid similarities to the gameplay style of The Legend of Zelda series. Some remnants of this larger quantity can be found in the final game's data, which includes an unused model for a Yoshi head nozzle and parameters for a sniper nozzle. While the former's properties are unknown beyond its appearance (with its model lacking any associated animations), the latter would have been 100 times more powerful than the Squirt Nozzle and would've had a significantly larger hitbox. However, it also would've required Mario to charge it like the Rocket Nozzle and Turbo Nozzle.