Despite the enormous technical and economic efforts to improve environmental conditions, currently about 40% of the global population (or 2 billion people) are still lack access to safe water supply and adequate sanitation facilities. Pollution problems and transmission of water- related diseases will continue to proliferate. The rapid population growth and industrialization will lead to a reduction of arable land, thus exacerbating the food shortage problems and threatening environmental sustainability. Natural systems in this context are a transdisciplinary approach which employs the activities of microbes, soil and/or plants in waste stabilisation and resource recovery without the aid of mechanical or energy-intensive equipments. Examples of these natural systems are: waste stabilisation ponds, aquatic weed ponds, constructed wetlands and land treatment processes. Although they require relatively large land areas, the natural systems could achieve a high degree of waste stabilisation and at the same time, yield potentials for waste recycling through the production of algal protein, fish, crops, and plant biomass. Because of the complex interactions occurring in the natural systems, the existing design procedures are based mainly on empirical or field experience approaches. An integrated kinetic model encompassing the activities of both suspended and biofilm bacteria and some important engineering parameters has been developed which could predict the organic matter degradation in the natural systems satisfactorily.