Our tonsils and nasal hair filters out air impurities. How does our body filter out water impurities?

Actually, your tonsils are part of the lymph system/immune system. Your tonsils are there to catch bugs as they go down your throat.

The biggest filter in your body is your liver. The liver metabolizes or breaks down everything, good or bad. Some of the stuff the liver puts out goes to your gall bladder and eventually back into you digestive track where it helps in digestion. The stuff your liver breaks down but leaves in the blood goes to your kidneys where it is selectively excreted or retained.

Your whole respiratory tract, not just your nasal passages are lined with mucous menbranes coated with sticky mucous that traps dust and microorganisms. Little hairs called cilia are constantly moving in waves that push the mucous up your throat. This is why you periodically have to "clear your throat", and get that wad of mucous out of your throat. Most of the time this mucous is then swallowed and the bugs are killed in the highly acidic stomach juices. So you see, the stomach is part of your defense system, too.

Water can be impure in several ways. It could have dirt in it, like drinking from a muddy river. It could have bacteria if it is contaminated by waste water like what happened when Hurricane Katrina caused flooding. It could also be chemically contaminated with high amounts of disolved salts and minerals.

Dirt just goes through the body with the undigested food and comes out the far end of the colon. Bacteria is killed by the stomach acid or by good bacteria that is always in our bodies. Chemicals are handled by the liver and kidneys.

our kiddneys filter the most of the water...but there is a certain amount of impurities that go into our cells via blood stream after the water intake goes through out digestive system

well your kidneys filter out all of the stuff your body isn't going to need or use. For example when beer is ingested your kidneys filter it out of your body thus the rapid peeing sensation when your drink beer.