To hire the work done it is going to cost $3-4 per square foot.

Are the "water stains" circular like from a pot or are they large irregular shaped stains? Are they mainly in high traffic areas? Is the wood raised, cupped, does it have excessive gaps?

What needs to be done is to resand and finish the floor. This is something that is better left to the pros, as you can do some serious damage if you are not careful.

To really clean the wood floor up nice, which you need to do before putting any more stain or polyurethane, etc., try the SNAP Heavy Duty Concentrate from the 'Home Care Store' at www.shopEZ.unfranchise.com. Also, if the 'water stains' are not from water, but organic, such as from a pet, get a bottle of one of the Global Care products from called 'Pet Magic' or 'SOS' from the 'BioTech store'. They remove any organic stain and order, even the old ones. This can be ordered online and shipped directly to you.