Place a layer of cotton batting to the bottom of your water cistern. Depending on the size of your cistern, you will probably need 1 or 2 inches of cotton batting lining the bottom of your cistern. Use more material for larger cisterns.
Add a layer (roughly 1 or 2 inches thick) of granulated activated charcoal. Purchase this charcoal at pool supplies stores or retailers that specialize in water filtration.
Place a layer of fine grain sand (roughly 1 or 2 inches thick) on top of the charcoal. Add a layer of large grain sand to the top of the fine grain sand.
Place a layer of fine grain gravel on top of the large grain sand layer. Follow this layer with a layer of large grain gravel. Repeat steps 3 and 4 until you have a relatively thick (about 1 foot) level of material to filter the water.
Test the filtration system. Pour water into your cistern and let it filter through the layers. The water should come out clear and clean. If you notice the water is not clean or clear, add more layers to your cistern.