Here are some basic steps to get lots of Rupees:
- Talk to the man west of Oshus's house. When he asks you to clear his garden, do that. He'll give you a Green Rupee x1. Then he'll show you the location for a tree. If you get to that tree, somersault into it. You'll find a Big Green Rupee x100.
- When you go to the Bomb Garden on Cannon Island, you can get a Shovel. In that same room, there is a spotted place on the dirt. Dig that area. You'll get a Big Green Rupee x100.
- If you meet Linebeck, you'll get a ship. After you get a cannon, enemies may start appearing on the sea. If you go on the sea, several monsters should appear. Try your best to shoot them. This can get you lots of Rupees if you shoot a lot of monsters.
- Cut grass on Mercay Island. You can get 30 Rupees in one minute. If you want to repeat, go into a house, then go out again.
- In Wayfarer's hideaway, you have to fight a serpent-like beast to proceed. Every time you kill one, you get a Red Rupee x20. You can use this to repeatedly get tons of Rupees.

Hope this works for you! If it does, please generously rate me thumbs-up.