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The present study assessed the effect of agricultural practices on biomarker response in white stork (Ciconia ciconia) nestlings from continental Croatia. During the breeding season of 2022, blood was sampled (n = 54) from the landfill Jakuševec and the agricultural areas Baranja and Srijem. Different patterns of biomarker response in regard to the sampling site were detected. Results demonstrate the presence of inhibitory pollutants from the landfill Jakuševec and agricultural area Baranja, which is reflected in lower cholinesterase (ChE) activity. Oxidative stress biomarkers show different responses concerning study sites. Glutathione reductase (GR) activity was higher in Baranja and Srijem, suggesting a different mixture of pollutants inducing an antioxidative response. Leachate from the landfill Jakuševec is suspected to affect the white stork nestlings by elevating the concentrations of reactive oxygen species (ROS). An environmental combination of pollutants appears to induce oxidative stress in white stork nestlings. In addition to agricultural practices, white stork nestlings may also be under environmental pressure from the surrounding pollution. Further research is warranted to include additional chemical analysis to associate the environmental concentrations with the potential adverse effects in apex predators, such as the white stork.