"I pull water out of my well at a cost of $1 per bottle." This is the same as buying a bottle of water from a supplier. Your input costs $1 per bottle. You sell it for $1 dollar. Your profit is zero and your margin is zero. (profit = revenue - cost of inputs // profit margin = profit / revenue )
"I later sell if for $5 dollars per bottle." If you were to buy from a supplier now because there is no ferry it would cost you $5 dollars per bottle. You then sell the water for $5 per bottle. Your profit is zero and your profit margin is zero. (profit = revenue - cost of inputs // profit margin = profit / revenue )
So your profit margin is still zero.
You have $400 dollars in your pocket though. Where does this come from - this comes from speculation. You "invest" in 100 bottles of water at $1 dollar. The market for water goes up so people are now willing to buy bottles of water at $5 dollars. You speculation profit = revenue - cost of inputs[where this is the prior cost for you]. The speculation profit is $400 dollars.
This is the answer to your other comment [ http://news.ycombinator.com/item?id=1118301 ].
These are two types of profit.
profit = revenue - cost (at the same time)
profit margin = profit / revenue
speculation profit = revenue - costs from an earlier time