The invention relates to a water purifying microbial ecosystem and application thereof. The water purifying microbial ecosystem comprises a porous filtering soil layer, wherein the porous filtering soil layer is formed by piling porous filtering soil materials made from volcanic ash based soil through firing and is a water-permeable filtering material with gap diameter being 0.1-4mu m, specific surface area per liter being 10,000-50,000m<2> and particle diameter being 1-10mm; and in addition, various nitrobacteria floras including nitrite bacteria, nitrifying bacteria and denitrifying bacteria flora are implanted in the porous filtering soil layer. According to the water purifying microbial ecosystem, the porous filtering soil material which has a large effective adsorption area and the general properties, such as ion exchange capability and containment of trace elements, of soil is adopted, and therefore the multiple nitrobacteria flora matters are suitable to be implanted into the porous filtering soil layer and the porous filtering soil material and meet the requirements for the growth and breeding of waterweeds and fish in ecological micro landscapes.