In a large, nonreactive stockpot, bring the bottled water to a boil over high heat. Meanwhile, working in small batches, place the ginger into a food processor and add 1 cup hot water to make mincing easier. Process until minced; pour the mixture into the pot. Continue until all of the ginger has been minced and added to the pot.
When the water comes to a boil, turn the heat off. Take the limes and with a spoon scoop the insides into the pot; drop the peels into the pot as well. Add the brown sugar and stir well to dissolve. Cover and let stand for 1 hour.
Strain the liquid through a fine strainer or a double layer of dampened cheesecloth. Pour through a funnel into containers. Store for up to 1 month, but try to use when fresh, as the potency of the ginger fades with time.