How Well Water Treatment and Whole House Water Filtration System Protect Against Contaminants? Well, water contains bacteria, lead, radon, and volatile organic compounds, and to protect you from these contaminants it's important to have suitable well water treatment systems. In the rural areas where municipal water supply is not available then well water is the best option as it is the cheapest way to deliver water into your home. If you want to have the most efficient well water treatment system then analyze the well water chemistry and must have a fundamental understanding.