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Critical transitions between ecosystem states can be triggered by relatively small external forces or internal perturbations and may show time-lagged or hysteretic recovery. Understanding the precise mechanisms of a transition is important for ecosystem management, but it is hampered by a lack of information about the preceding interactions and associated feedback between different components in an ecosystem. This paper employs a range of data, including paleolimnological, environmental monitoring and documentary sources from lake Erhai and its catchment, to investigate the ecosystem structure and dynamics across multiple trophic levels through the process of eutrophication. A long-term perspective shows the growth and decline of two distinct, but coupled, positive feedback loops: a macrophyte-loop and a phosphorus-recycling-loop. The macrophyte-loop became weaker, and the phosphorus-recycling-loop became stronger during the process of lake eutrophication, indicating that the critical transition was propelled by the interaction of two positive feedback loops with different strengths. For lake restoration, future weakening of the phosphorus-recycling loop or a reduction in external pressures is expected to trigger macrophyte growth and eventually produce clear water conditions, but the speed of recovery will probably depend on the rates of feedback loops and the strength of their coupling.