Energy flow is a central characteristic in all ecosystems, and it has attracted considerable scientific attention due to its significant effects on the stability of food webs. Lake ecosystems that undergo regime shifts (clear water phase, phytoplankton dominated changed into turbid water, macrophytes dominated or vice versa) are characterized by a series of transformation in trophic structure. Although previous studies have mainly focused on the causes and consequences of regime shifts in shallow lakes, studies about responses of energy flow changes to regime shifts is far from complete. In this paper, we estimated trophic position and benthivory (i.e. degree of benthivory) of seventeen fish species from seven shallow lakes. Our data show that the trophic position and benthivory of fish species in clear water phase are significantly higher than in turbid water. This finding might help spark some ideas for subtropical lake eutrophication treatment.