A gy6 will never be water proof like a 4 wheeler. The biggest problem is the cooling fan on the side sucking air in will also suck water in and flood the open charging system behind it. Best you can do is to try to make it splash proof and avoid any water more than motor deep.
I did replace all the electrical connectors on mine when I rewired it with water proof ones.
https://www.ebay.com/itm/Waterproof-...tors.TRS0.TSS0
Be warned they require a special (about $20) crimper to terminate them correctly.
https://www.ebay.com/itm/MUYI-SN-48B...sid=m570.l1313
I also swap them on my 4 wheelers because they are better than what most come with and last longer. I do ride along on mud rides with the buggy time to time but it's limited to splashing along dodging deep holes while they are playing submarine.