I agree with Sunnie. Sunnie and I are both breeders - we've raised more than a few puppies
Feed earlier in the day and remove the water at night.
Puppies DO NOT need water throughout the night. IF he does NEED it, there is a different and more serious underlying problem that needs to be address by the vet.
Puppies generally poop shortly after their meals. This is a carry over from when they were new born. Immediately after nursing (often during) mom will lick their bottoms to encourage elimination. Without the licking, they wouldn't poop. When we have to hand raise puppies we have to wipe their bottoms with warm rag to get them to poop. This "habit" quite often will remain with the dog throughout their lifetime (my 12 year old still poops immediately after a meal). So if you feed her earlier, she should poop for you well before bedtime.
Good luck!