Soil microbial communities play an essential role in riparian ecosystems, which commonly consist of a few abundant taxa and numerous rare taxa. However, relatively little is known about the community assembly processes of abundant and rare taxa, and how these respond to fluctuating environments. In this study, patterns and drivers of the assembly processes for abundant and rare bacterial and archaeal subcommunities in a riparian zone were determined. Results showed that the community structures of abundant and rare bacteria and archaea exhibited a consistent variation along the riparian elevation, which was highly associated with flooding frequency. Rare taxa were phylogenetically more closely clustered, but occupied narrower niche breadths than abundant taxa. The community assembly of abundant and rare bacteria was driven respectively by dispersal limitation and variable selection; undominated processes and dispersal limitation dominated abundant archaeal community, while rare archaea was primarily governed by homogeneous selection. Soil moisture and ratio of time soil was submerged to exposed to air were the two most decisive factors for the assembly processes of both rare bacteria and abundant archaea. The assembly processes of rare bacteria were also significantly associated with soil NH4+, Fe2+ and Fe2+/Fe3+, while rare archaea were significantly associated with C/N and total carbon. Here, flooding may influence community assembly processes by shaping soil niches and imposing disturbances. Overall, this study reveals divergent assembly processes for abundant and rare subcommunities in the riparian zone, which is essential knowledge to further elucidate the stability and maintenance of ecosystem functions under changing environments.