Low-Key Lysmith: Where did all the water go? What a silly question... after being on the ark all that time, all the animals would be thirsty! The rest of the water is still in circulation today, order a glass of the 'house' wine in any pub!
As for the build up of manure, that wouldn't be a problem - it's a well known fact that it's virtually impossible to do a 'number two' in front of a stranger... so basically they held it in. Proof of this is easy to find - as most animals can cross their legs.
Many wonder how Noah got all the insects on board - well that's easy. Most were captured the night before the flood, as he accidentally left a light on in the ark, the remaining insects were collected during the heat of the next day by leaving a small strawberry cheesecake on the roof of the ark.
It seems also you guys don't understand how the ark 'got about'... come chaps, use your heads! Basically Noah glued all the birds feet to the roof of the ark, a special opening on the North, East, South and West would of been created just big enough for a Giraffe holding a bag of chips to put his head through - the birds would try to fly to get the chips, thus giving directional control.
If I've missed anything, just let me know... I'm here to help.