Water-based stains offer better indoor-air quality and a different aesthetic, but applying them requires an experienced professional There is a critical question you should put to your hardwood flooring contractor if you are planning to finish your floor with a water-based stain: Does he know how to apply it? The question is easily overlooked. Most of us would assume this knowledge is a given. But applying water-based stain requires a different technique than what is used with traditional oil-based products. And so can applying a water-based polyurethane over the water-based stain. If you try to use these stains like traditional products, you most likely will not be happy with the final appearance of your floor. And you will face the costs of refinishing in order to fix it.