Multitrophic indicators reveal replacement-driven community reassembly in urban-dominated and mountainous river systems of Beijing, China

Urban expansion and hydrological disturbance are reshaping river ecosystems worldwide, yet their relevance for ecological indicators across trophic levels remains insufficiently resolved. We compared phytoplankton, benthic macroinvertebrate, and fish communities between urban-dominated and mountainous river systems in northern Beijing during spring and autumn 2025. By integrating community composition, beta-diversity partitioning, fish functional diversity, and environment–community analyses, we examined how multitrophic community patterns differed between contrasting river contexts and how autumn patterns were expressed following a major regional flood. Community responses were trophic-specific: phytoplankton showed pronounced seasonal turnover, fish showed a weak autumn tendency toward urban–mountain differentiation, and benthic macroinvertebrates displayed more context-dependent seasonal responses. Across all trophic levels, urban–mountain differentiation was dominated by turnover rather than nestedness, indicating that urban-dominated communities were not simply species-poor subsets of mountainous communities but assemblages characterized mainly by species replacement. Fish communities in urban-dominated reaches also showed reduced functional richness, suggesting a narrower range of ecological strategies in these river contexts. The autumn survey followed the Haihe “25·7” regional flood, which affected the Chaobai River basin and the Bai River flowing through Yanqing. In this post-flood autumn context, within-group heterogeneity was higher in some urban-dominated assemblages, whereas measured nutrient variables explained only a limited proportion of multitrophic community variation. These patterns are consistent with possible disturbance-related reorganization superimposed on longer-term differences between river contexts, but they should not be interpreted as direct evidence of flood causation or as a strict causal test of urbanization. Overall, our results show that taxonomic, beta-diversity, and functional metrics provide complementary indicators for assessing river ecosystem reorganization under interacting urban and hydrological pressures. These findings support multitrophic, multi-season, and context-aware biomonitoring, and highlight the importance of conserving mountainous headwaters while restoring habitat complexity, ecological flow, and longitudinal connectivity in urban-dominated rivers.