Selling Treasure:
Many of the treasures you find, especially those salvaged from the sea, are primarily for selling. While some might be ship parts, others are simply valuable items like gems or ancient artifacts. Always check the value of your treasures at a shop before selling. Prioritize selling high-value items if you're in need of Rupees for ship upgrades or other purchases.
Mini-games for Profit:
Several mini-games, such as the Shooting Gallery or the Beetle Island maze, offer Rupees as rewards for high scores. Once you've mastered a mini-game, you can replay it repeatedly to farm Rupees efficiently. This is often a more reliable method than simply hoping for enemy drops.
Fishing for Rupees:
As mentioned in the side quests, catching and selling fish can be a steady source of income. Different fish have different values, so learn which fish are most profitable and where to catch them. Some rare fish can fetch a high price.
Breaking Pots & Cutting Grass:
The classic Zelda method of finding Rupees still applies. Always break pots, cut tall grass, and smash rocks. While individual rewards might be small, they add up over time, especially in dungeons or areas with many destructible objects.