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Purpose: This research is expected to shed light on soil contamination in citrus orchards and provide a reference for soil quality maintenance and improvement in orchards under the organic fertilizer substitution scenario. Materials and methods: Heavy metals (HMs) and veterinary antibiotics (VAs) in soils collected from citrus orchards in Meishan, Sichuan Province, China, were measured. Single factor index, potential ecological risk factor, and potential ecological risk index were employed to assess the contamination status and potential ecological risks of HMs in soils. Additionally, the risk of VAs was also evaluated based on their risk quotient values. Furthermore, Pearson's correlation analysis, hierarchical cluster analysis, and principal component analysis were employed to identify the potential sources of HMs and VAs in soils. Results and discussion: HMs and VAs exhibited great variance in the study area. Nickel (Ni) was the primary metallic contaminant, followed by cadmium (Cd), chromium (Cr), and arsenic (As). HMs accumulation in soils would not pose risks to the ecosystem. Atmospheric deposition and livestock manure could be the primary sources of HMs in soils. In terms of VAs, fluoroquinolones (FQs), sulfonamides (SAs), and tetracyclines (TCs) were the major VAs in soils, with the accumulative level averaged at 84.6 μg kg−1 (36.8–369 μg kg−1). Additionally, the residual VAs, except for enrofloxacin (ENR), would only pose limited to moderated risk to soil microbes or aqueous organisms. Conclusions: Clean and high-quality organic fertilizers, instead of livestock manure, were recommended to eliminate the potential environmental risks during organic fertilizer substitution. [ABSTRACT FROM AUTHOR]