The invention relates to a method for establishing biodiversity in rivers and lakes, which comprises the following steps of: selecting key species and key points of a recovery area; the key point is that natural regression and enrichment of key species are promoted through a combined technology of dam field, water quality improvement, bottom mud diversity improvement, putting of a porous material adsorbed with a microbial agent, original living sludge and algae species to construct a biological bed and underwater habitat, small-range biological diversity is formed, and large-scale development of biocenosis is controlled; then, the key point is used as a biological source, water quality improvement, alien species management and control and overflow organism expansion and ecological succession of the whole restoration area are matched, water area ecological restoration can be more purposeful, the habitat is continuously used as a species source, a large number of overflow organisms are continuously transformed and restored, and the ecological restoration effect is achieved. The water ecological condition of the whole restoration area is improved through radiation, the biodiversity of the whole restoration area is restored, and the method can be applied to river and lake water quality improvement, water body environment improvement and water area biodiversity restoration.