The degradation, alteration and depletion of riparian habitats caused by river regulation are among critical conservation concerns. Aquatic and riparian habitats support not only river-dwelling biota such as macroinvertebrates and fish, but also waterbirds, the top predators in the aquatic food web. Despite the intimate relationships between fish and waterbirds, the two groups are often investigated separately. Using an integrative approach, we examined the effects of dams on fish and scaly-sided merganser (Mergus squamatus), an endangered, iconic riverine species, where the lack of knowledge about habitat preferences greatly hampers long-term conservation efforts. Our analysis quantified three causal links: (1) water depth had direct, comparable, negative effects on both fish and waterbirds, and the path coefficients for fish and birds are –0.31 and –0.46, respectively; (2) river landscape heterogeneity directly and positively affected fish and waterbirds, and the path coefficients for fish and birds are 0.63 and 0.19, respectively; and (3) depth and river landscape also exerted indirect effects on waterbirds through their impacts on fish abundance, and the path coefficients for fish and birds are –0.15 and 0.28, respectively. Our findings could contribute to the rational spatial planning and sustainable operation of dams in that maintaining instream habitat availability and heterogeneity would benefit the whole riverine ecosystem.