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• Ecosystem multifunctionality was higher in rhizosphere soils than in bulk soils. • Ecosystem multifunctionality was mainly determined by environmental factors. • C cycling and N cycling varied among microhabitat and macrohabitat types. The importance of plant and soil microbial diversity in sustaining ecological functions has attracted considerable attention. However, little is known about how these factors jointly affect the ability of an ecosystem to provide multiple ecological functions simultaneously (i.e., ecosystem multifunctionality [EMF]) in natural environments, especially in wetlands. Here, we collected rhizosphere soils, bulk soils, and sediments (microhabitats) from riverine, lacustrine, and palustrine wetland sites (macrohabitats) across the remote Tibetan Plateau. Plant diversity (taxonomic, phylogenetic, and functional) and soil bacterial diversity (taxonomic and phylogenetic) were determined. We also calculated EMF using 20 variables related to soil carbon cycling, nitrogen cycling, and plant productivity. The results showed that EMF was significantly higher in rhizosphere soils than in bulk soils, but no significant differences were detected among the macrohabitat types. A significant relationship between EMF and bacterial diversity was detected only in rhizosphere soils, and a positive relationship between EMF and plant diversity was found in riverine and lacustrine wetlands. Environmental factors (climate and edaphic properties), bacterial diversity, and plant diversity together explained 63.48% of the EMF variation. Path modeling revealed that the effects of macrohabitat and microhabitat on EMF were mediated mainly through edaphic properties and bacterial diversity, respectively. These results significantly advance our understanding of the patterns and drivers of EMF in wetlands and are also critical for predicting changes in wetland functions in response to biodiversity loss and anthropogenic activities. [ABSTRACT FROM AUTHOR]