- Anything (except for heart piece replacements and treasure chests with a mask you already have) that normally gives you a recovery heart gives you a green rupee instead if you have full health.
- There are 3 nonrenewable red rupees in the river in the laundry pool only on the night of the second day.
- Tingle is only in North Clock Town in the day and if you buy the Clock Town map before the Woodfall map as a deku, he will go back into the air right away and you have to burst his balloon again to buy the Woodfall Map.
- If you chop all the bushes in a jumping bunch of bushes all at once with the great spin attack, one of them will release a red rupee.
- Every time you talk to the zora at the top of the slope in zora hall in zora form, they ask you for a pictograph of Lulu and if you give them one, you get a red rupee.
- Bushes sometimes release fairies when Link's health is extremely low.
More secrets can be found at The Legend of Zelda: Majora%27s Mask Secrets.