<p>Salinization is increasingly posing a serious threat to the maintenance of aquatic microbial biodiversity and/or functionality. However, little is known about the assembly processes that govern microbial communities in large spatial‐scale aquatic ecosystems with varying salinity levels. Herein, we investigated the differences in the spatial distribution, environmental adaptation, co-occurrence patterns, and ecological assembly mechanisms of microbial communities between nonsaline and saline water on a global scale using the Earth Microbiome Project (EMP) dataset. Our results presented that the nonsaline water microbial community exhibited higher alpha diversity than the saline water counterpart, and significant differences in the microbial composition and structure were observed between nonsaline and saline water. Nonsaline water species exhibited broader environmental thresholds and stronger phylogenetic signals of ecological preferences in comparison with saline water species. Network analysis revealed that the nonsaline water microbial network exhibited higher complexity and stability compared with the saline water one. In addition, stochastic processes were predominantly responsible for the microbial community assemblies in nonsaline water (62.97%) and saline water (60.20%). Interestingly, temperature and salinity were the primary determinants influencing the balance of stochastic and deterministic processes in nonsaline and saline water microbial communities, respectively. These findings underscore the critical role of salinity in regulating microbial community dynamics, which could inform future conservation strategies to mitigate biodiversity loss in aquatic ecosystems threatened by increasing salinization.</p>