Ecological regime shifts typically result in abrupt changes in ecosystem structure through several trophic levels, which leads to rapid ecosystem reconfiguration between regimes. An interesting aspect of the impact of regime shift is that alternative regimes may induce distinct shifts in energy pathways; these have been less tested than structural changes. This paper addresses this by using stable isotopes to establish the energy pathways in fish communities. We specifically focus on the impact of regime shift on changes of the energy pathways, and how the magnitude and direction of these changes affect the local community. We found that energy pathways significantly varied among the planktivorous, benthivorous, and piscivorous trophic guilds as a result of the alternative regimes. The regime shift from a clear to a turbid state altered the food web towards planktonic energy pathways and truncated food chain length, which is indicative of less ecological efficiency. This was confirmed by the adaptive foraging strategies of prevalent omnivores in the current communities. These structural and functional characteristics of trophic interactions might not facilitate classic trophic cascading effects in such a turbid regime and suppress the system's response to environmental changes, e.g., nutrient loading, and restoration efforts in turbid to clear water regime shifts.