<p>Restoration of degraded estuarine wetlands relies heavily on rhizosphere bacterial communities that support vegetation colonization and persistence. However, the mechanisms driving microbiome assembly across soil–plant continua in these fragile ecosystems remain poorly understood. Here, we examined plant traits, soil physicochemical properties, and α-diversity and community structure in rhizosphere and non-rhizosphere soils of two dominant species (<i>Suaeda salsa</i> and <i>Phragmites australis</i>) in a degraded estuary in China. We further assessed bacteriome assembly processes, β-diversity, and the relative influence of abiotic and biotic factors. Bacterial community structure differed significantly between the two plant continua, though diversity did not. Across both rhizosphere and non-rhizosphere soils, bacteriome assembly was governed predominantly by heterogeneous selection. Within this deterministic framework, intrinsic biotic factors—including keystone taxa, metabolic functions, and host plants—exerted stronger effects on community assembly than abiotic drivers. Moreover, available phosphorus facilitated this assembly pattern through indirect pathways. These findings highlight the pivotal role of biotic interactions in shaping bacteriomes and maintaining functional stability in fragile estuarine ecosystems, with implications for guiding ecological restoration.</p> Graphical abstract <p></p>