Wetlands are ecologically critical ecosystems increasingly impacted by anthropogenic disturbances. Understanding how disturbance shapes plant communities via soil conditions, functional traits, and biodiversity is essential for wetland conservation. Here, we aimed to examine how disturbance intensity shapes soil-plant interactions and multidimensional biodiversity in a protected wetland. We surveyed four zones of the Crested Ibis National Nature Reserve (Shaanxi, China) along a disturbance gradient defined by zoning categories and field indicators such as vegetation degradation and human activity. Results showed that disturbance significantly altered soil nutrients, salinity, and stoichiometry, especially increasing N:P ratios and conductivity in highly disturbed zones. These shifts corresponded with trait changes from acquisitive to conservative strategies (e.g., reduced SLA, increased LDMC and C:P, N:P). While species richness peaked under high disturbance, functional diversity (FRic, FDis, Rao’s Q) and Faith’s PD were highest at moderate levels. MPD and MNTD increased under moderate to high disturbance, indicating reduced filtering and greater stochasticity. PCA, RDA, regression, and SEM supported these findings, highlighting soil-mediated effects on trait expression and diversity patterns. Our findings suggest that moderate disturbance enhances functional and phylogenetic diversity, promoting ecosystem resilience through greater niche and evolutionary space. Excessive disturbance, however, leads to homogenization and instability. Integrating trait-based and phylogenetic perspectives supports adaptive, low-intensity management to sustain wetland biodiversity and multifunctionality.