The application of chemical pesticides is one of the main practices in citrus orchards. But during this operation, a considerable amount of sprayed volume is emitted to off-target areas using air-blast sprayers. The present study aimed to investigate pesticides' toxicological impacts in citrus orchards through determining the proportion of pesticides in different areas (air, soil, and canopy), which facilitate toxicity assessment of pesticides in citrus orchards. In this study, human toxicity and freshwater ecotoxicity impacts were assessed using USEtox 2.1 modeling approach for five active ingredients used in citrus orchards in the south of Iran. Different spraying scenarios were defined based on two types of nozzles (Hallow-cone and Teejet full-cone) and three levels of pressure (30, 40, and 50 bar) in two orchards with different row spacing. Results showed that only 26–37% of spray solution is deposited on the target with much loss to areas between tree canopies on the row. Scenario 1 (Hallow-cone nozzle with spraying pressure as 30 bar) shows the highest spraying efficiency in the both orchards (37% and 34% for Tangerine and Lemon orchards, respectively). Air emissions were obtained around 17 and 18% for hollow-cone and Teejet full-cone nozzles, respectively. The final inventory was obtained considering evaporation rate of active ingredients from soil surface and leaves. Based on the results obtained from toxicological impact assessment, Thiacloprid and Carbendazim had the highest negative environmental impacts on human health and freshwater aquatic ecosystem, respectively. Based on the results, soil emissions were identified as more critical than air emissions in terms of environmental consequences. It can be attributed to the higher characterization factor and deposition on the soil in comparison to the air. The present study provided well-founded information on the environmental performance of production systems by estimating the relevant emissions of pesticides to different compartments and determined the human and freshwater toxicity impact profiles, which assist decision-makers and LCA-practitioners to have a better perspective about pesticides behavior in receiving compartment.