Reputation Points are similar to XP Points you get on the Main Farm - they help you to upgrade your Reputation Level. The higher your Reputation Level, the more Secret Spring content you can unlock (new recipes in machines, new decorations, new animal habitats, etc.)

You can earn Reputation Points by harvesting Water Crops and completing orders at Noni's Trade Post.

Check your Reputation Level in top right corner of your game screen (while in the Secret Spring).