The bacterial community structure and transmission dynamics across three habitats-riparian zone (H), water (W), and sediment (S) were examined in Hongliugou, Ningxia, throughout autumn and spring. Analyses were performed utilising 16S rRNA gene high-throughput sequencing in conjunction with PCoA (principal coordinate analysis), Venn diagrams, β-diversity partitioning, NCM (neutral community models), ternary plots, and co-occurrence networks. In total, more than 30 000 OTUs (operational taxonomic units) were identified. α-diversity exhibited the hierarchy H>S>W, with total diversity being greater in autumn than in spring. At the phylum level, Proteobacteria were predominant, with Bacteroidota, Actinobacteriota, and Cyanobacteria. PCoA demonstrated substantial differentiation among the three habitats over the seasons. Seasonality markedly affected transmission patterns. during autumn, W and S exhibited a close relationship, whereas H maintained relative independence, with community variations predominantly influenced by nestedness. In contrast, during spring, H and S exhibited a tendency to converge with increased contributions from S to W, whereas β-diversity partitioning revealed that species turnover predominated, comprising around 75%. The NCM fit was superior in autumn (R²=0.547) compared to spring (R²=0.324), indicating that stochastic processes were more influential in autumn, whereas environmental filtering and deterministic selection were more pronounced in spring. Autumn demonstrated a stable co-occurrence network characterised by strong modularity and minimal inter-module interchange, whereas spring revealed enhanced connectedness and frequent cross-niche transmission. The comprehensive examination of Venn diagrams and ternary plots revealed “H→S→W” as the principal migration channel, with sediment serving as a crucial intermediary. This work characterises the structural and niche features of bacterial communities across various environments, elucidating the transmission dynamics along the W-S-H continuum and offering a scientific foundation for enhancing soil and water conservation strategies.