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In water-deficient area, river-changed ponds are common and vital for aquatic species. This paper studies the relationship between the environmental factors and the benthic invertebrate communities in varying ponds under river habitat modifications (RHM). For analysis, numerous samples are collected from river-changed ponds in Beijing, China. These ponds are classified into five types, including totally reinforced ponds, channel reinforced ponds, bank reinforced ponds, natural ponds, and restored ponds. Results indicate: 1) the biodiversity of benthic invertebrates is dependent strongly on the pond type; 2) habitat quality explains a considerable amount of variations in benthic invertebrate communities, and RHM show strong power in explaining variations in habitat quality; 3) RHM on the pond bank has stronger impact on the habitat quality than that on the pond bottom. These findings suggest that RHM can affect the benthic invertebrate community through changing the habitat quality. And we suggest that ecological restoration of pond bank should be a useful way to improve invertebrate biodiversity for rive-changed ponds in Beijing.