For the bottled water - yes, there's a charge. BUT there's no need to buy it as the water from the tap is distilled and is as good if not better than the bottled kind. Believe this is true for most lines.
I cruise the Emerald Princess, Eastern Caribbean on April 16, 2012
You won't be charged for coffee. Some ships do have specialty coffees and might charge for that now (HAL didn't on our cruise a few years back) but morning coffee/tea from room service, buffet or the dining room are no charge. Same for dinner.