Abstract The effectiveness of Aoki's entropy production indices as ecological indicators of the trophic state is tested here under the changing hydrological conditions of Lake Trasimeno, a shallow freshwater lake in Italy. The analysis leads to a review of Aoki's indices and a definition of a new set of eutrophication indices ( c, d, d′) based on the entropy production per surface unit rather than volume unit, which seem to be good ecological indicators for the trophic state of lake ecosystems. The positive correlation between these indices and the trophic state of a small set of lakes suggests that they are able to take into account the influence of the biological productivity on the whole entropy production of the systems. Moreover, the indices d and d′ show a good negative linear correlation to the lake mean depth, showing the importance of this morphological parameter in the eutrophication process or succession in lakes. The values of the indices show that Lake Trasimeno exhibits a trophic state consistent with Carlson's TSI indices and with the results previously obtained by the application of Vollenweider's eutrophication model based on phosphorus loading and the Hillbrich–Ilkowska method, but less compliant with the Vollenweider–OECD classification criterion. The study emphasises the importance of a holistic thermodynamic approach in getting new insight into the fundamental mechanisms of the ecological succession of lake ecosystems.