How bad is the water damage

@kiddoz the very first thing you want to do, is to no LONGER doing this "But now my 3Ds can charge has the light but then flash and then I hear a pop sound". You are potentially making a bad situation worse by continuing risking short circuiting the rest of the board.

The next thing to do is to clean it. Disassemble your Nintendo by using these guides. You must remove all EMI shields. If you do not remove those, you might as well not do anything. After you removed those, clean the whole board, connectors and all with +90% isopropyl alcohol. Follow this guide , and even so it was written for an iPhone all the points are still pertinent to your console. While you clean your board, check for any obvious damage, like burned or missing components etc. When it is properly cleaned, replace the battery. All these steps are to avoid delayed failure caused by corrosion. Best thing to do would be to clean it with an ultrasonic cleaner, but if you do not have access to one, this will at least help. Once all this is done, reassemble your Nintendo and reevaluate. Until it is cleaned, everything will only be a guess. Even with all this, water damage has only a small chance to be fully repaired, but at least you can give it a try. The popping sound and turning off is usually related to torn flex cables. Make sure you check those properly as well

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