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Transitional water ecosystems can be exposed to high levels of anthropic pressure. The main aim of this study was to present the ‘Capo Peloro’ lakes (southern Italy) case study, which highlights the advantageous use of ecotoxicological biomarkers in key copepod species, to reveal potential contamination in transitional water ecosystems. The focus was on changes that occur after the summer season, as during the summer, the surrounding human population increases significantly, with the consequent enhancement of anthropic pressures. Biomarkers were defined to monitor the zooplankton copepods Paracartia latisetosa, Acartia tonsa and Oithona brevicornis. Acetylcholinesterase, lipid peroxidation, and benzo(a)pyrene-monooxygenase activities were determined. P. latisetosa, A. tonsa and O. brevicornis show linear increases in their acetylcholinesterase activities with increasing concentrations in sample homogenates, which defines their high metabolic rates, and thus the suitability of these species as bioindicators. Biochemical alterations in these species induce changes in their biological attributes that can also lead to their disappearance, with a cascade of consequences for the higher trophic levels in the food chain. These data indicate that for the two lakes of Capo Peloro there is contamination by pesticides, carbamates and polycyclic and polyhalogenated aromatic hydrocarbons. This occurs mainly at the end of the summer season, and only affects the species of the low trophic levels. This case study shows the benefits provided by this biomarker approach as applied to zooplankton species, to monitor transitional water ecosystems and to estimate their toxicological risk, and thus to provide an early warning signal for loss of ecosystem integrity.