AbstractMicroorganisms play important roles in soil biogeochemical processes, but the relative contributions of different microbial members in soil nutrient cycling and community maintenance are unclear especially in wetland soils with water‐level fluctuation. Here, soil samples, collected from severe inundation zone (SIZ), wet–dry cycling zone (WIZ), and arid zone (NIZ) of the lakeshore wetland of plateau lake Caohai, were used to investigate the relative contributions of core and rare taxa in maintaining nutrient cycling and their associations with microbial network. Results showed that WIZ exhibited higher extracellular enzyme activities including β‐1,4‐N‐acetylglucosaminidase, L‐leucine aminopeptidase, and acid phosphatase, the level of multi‐nutrient cycling and core microbial diversity compared with the NIZ and SIZ. The values of topological features (i.e., links, average degree, clustering coefficient, and graph density) were also higher in the WIZ compared with the NIZ and SIZ. Moreover, the core taxa, specifically their community structures, were the most important driver for multi‐nutrient cycles of wetland soil. Among these taxa, Sphingomonas, Bradyrhizobium, Mortierella, and Fusarium as the most abundant taxa in lakeshore wetlands were significantly positively correlated with most extracellular enzymes. By contrast, rare taxa showed higher degree and its subnetwork complexity than those of core taxa, which potentially serve as the species pool of core taxa to maintaining the microbial community stability. In conclusion, our study suggested that core taxa play dominant roles in soil nutrient cycles, while rare microbiota could greatly influence microbial interaction under hydrological changes.