Engine problems

Hoping for a tip I have a Suzuki Df90 that I had been running at a higher rpm in neutral for about 20 minutes after needing a boost to start it ran great for about 20 minutes before it started to run rough and stalled then wouldn't stay running prior to this the bilge pump had been running until the battery died as a result of these crazy storms up north I am thinking a fuel water issue but am not sure why other opinions