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Antibiotic resistance genes (ARGs) are a well-known environmental concern. Yet, limited knowledge exists on the fate and transport of ARGs in deep freshwater reservoirs experiencing seasonal hydrological changes, especially in the context of particle-attached (PA) and free-living (FL) lifestyles. Here, the ARG profiles were examined using high-throughput quantitative PCR in PA and FL lifestyles during four seasons representing two hydrological phenomena (vertical mixing and thermal stratification) in the Shuikou Reservoir (SR), Southern China. The results indicated that seasonal hydrological dynamics were critical for influencing the ARGs in PA and FL and the transition of ARGs between the two lifestyles. ARG profiles both in PA and FL were likely to be shaped by horizontal gene transfer. However, they exhibited distinct responses to the physicochemical (e.g., nutrients and dissolved oxygen) changes under seasonal hydrological dynamics. The particle-association niche (PAN) index revealed 94 non-conservative ARGs (i.e., no preferences for PA and FL) and 23 and 16 conservative ARGs preferring PA and FL lifestyles, respectively. A sharp decline in conservative ARGs under stratified hydrologic suggested seasonal influence on the ARGs transition between PA and FL lifestyles. Remarkably, the conservative ARGs (in PA or FL lifestyle) were more closely related to bacterial OTUs in their preferred lifestyle than their counterparts, indicating lifestyle-dependent ARG enrichment. Altogether, these findings enhanced our understanding of the ARG lifestyles and the role of seasonal hydrological changes in governing the ARG transition between the lifestyles in a typical deep freshwater ecosystem., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2022 The Authors.)