Wastewater treatment using waste materials (refuse concrete, waste paper and charcoal) and natural indigenous rocks (andesite, limestone, granite and nitrolite) in the form of multilayer media was investigated. The removal of suspended solids (SS), phosphate ion, nitrate ion, ammonium ion, toxic metals and chemical oxygen demand (COD) were evaluated for the multilayer wastewater treatment system. Effective removal of heavy metals such as cadmium, chromium, mercury and lead was demonstrated. SS and phosphate ion were removed with relatively high efficiency and the COD after treatment was lessened using certain combinations of media. The present wastewater treatment system is simple, convenient and low cost. Therefore, this method can be applied in small scale plants for wastewater treatment in local and nonexclusive areas.