Currently, dam construction is a main and growing global anthropogenic disturbance on rivers. Dams have major effects on the physics, chemistry, and biology of the original river, including altering water circulation and retention time, sedimentation, nutrient biogeochemical cycling (especially greenhouse gas emissions), and the amount and composition of the organisms present. Among those, the effect of dams on the riverine material cycle and ecology is especially concerning because of its close relationship with current global environmental problems such as climate change and ecological deterioration. This review thus mainly focuses on nutrient cycling and ecological changes in a regulated river. In the future, research on reservoir–river systems should focus on (1) processes and mechanisms of nutrient biogeochemical cycles, (2) interaction between these processes and ecological change such as phytoplankton succession, and (3) developing mathematical functions and models to describe and forecast these processes and their future interactions.