Hydro-environmental and ecological effects of drop structure in urban river system

• Drop structures significantly alter sediment microbial communities. • Drop structures increase microbial interaction complexity and reduce community stability. • Water velocity below drop structures correlates with microbial community structure. • Dual-drop configurations enhance nitrification potential more than single-drop. Drop structures are common in urban rivers, yet their ecological effects on sedimentary bacterial communities insufficiently resolved. We investigated nine artificial units (single- and dual-drop configurations) along the urbanized Yangmei River, China. Using 16S rRNA sequencing, co-occurrence networks, assembly modeling, and PICRUSt2 functional inference, and we evaluated microbial diversity, interaction architecture, assembly mechanisms, and N/P-cycling potential. The Mantel test results indicated a significant correlation between water flow velocity downstream of the drop structure and the benthic microbial community ( p < 0.05). Downstream networks were more connected but less modular and contained fewer keystone taxa, indicating higher interaction complexity yet lower compartmentalization and, by inference, reduced stability to disturbance. Stochastic processes overall dominated community assembly; in sediments, dispersal limitation prevailed but weakened downstream, where homogeneous selection increased, consistent with enhanced mixing across the drop. Functional profiles suggested a systematic rise in nitrification potential downstream in both configurations, with stronger gains in dual-drop units, whereas gene sets associated with DNRA and nitrogen fixation generally declined; phosphorus-cycling markers were comparatively insensitive. In single-drop reaches, a lower (nirK + nirS)/ nosZ ratio pointed to a reduced propensity for N 2 O accumulation. These patterns indicate that drop structures can restructure sediment microbiomes and shift N-cycle potentials toward nitrification, potentially elevating nitrate accumulation risks under sustained nutrient loading, while possibly limiting N 2 O buildup in certain settings. As gene imprints reflect potential rather than process rates, targeted assays are warranted to quantify biogeochemical outcomes and inform eco-hydraulic design.