Zooplankton are ubiquitous in aquatic ecosystems and play crucial roles in material cycling and energy flow. However, the mechanisms governing zooplankton community assembly, particularly habitat-specific differences, remain poorly understood. In this two-year study, we monitored zooplankton communities across reservoir and river habitats within the Chayuan watershed, a representative karst region in southwest China. Our findings revealed significant spatial divergence in water-quality variables (including water temperature, pH, total nitrogen, total phosphorus, permanganate index, dissolved oxygen, chlorophyll-a, and ammonia nitrogen) between habitats. Twenty-nine dominant zooplankton species were identified in reservoir and river communities, with only eight shared between the two habitats. The mechanisms underlying the corresponding zooplankton community structures showed distinct segregation between habitats, with deterministic processes predominating in reservoir communities (explaining 25.1% of the variation) and stochastic processes predominating in river communities (3.4% of the variation explained). Environmental drivers differed substantially between habitats: reservoir communities were primarily influenced by total nitrogen, dissolved oxygen, and chlorophyll-a concentrations, whereas river communities responded predominantly to ammonia nitrogen levels. This study provides novel insights into the divergent mechanisms governing zooplankton community assembly in lentic versus lotic systems within a shared karst watershed, offering theoretical foundations for ecosystem-specific management strategies in fragile karst environments. Future research should focus on key climatic variables (e.g., extreme precipitation) and hydrological dynamics (such as flow velocity and water residence time) to further elucidate the mechanisms behind zooplankton community assembly, providing deeper insights to facilitate effective ecosystem management in karst environments.

Continuous damming in karst rivers fragmented the longitudinal structure of river systems, disrupting plankton habitats, limiting dispersal, and reducing biodiversity. This study examined variations in zooplankton functional diversity in a dammed river system during dry and wet seasons. Sampling across both seasons yielded 44 samples, with 64 zooplankton taxa categorized into seven functional groups based on their traits. Functional diversity indices were calculated. Results revealed significant differences in nutrient concentrations between upstream and downstream sections, particularly during the dry season (R² = 0.11, p < 0.01). Zooplankton functional diversity decreased from upstream to downstream, with more pronounced differences in the dry season (R² = 0.94, p < 0.05), driven by reduced dispersal stochasticity (β_BC close to −1). Continuous damming primarily affected smaller zooplankton, such as rotifers, while dissolved oxygen, water temperature, and pH influenced distribution patterns related to habitat depth, breeding season, life span, and reproduction. These findings underscored the impact of damming on zooplankton functional diversity and informed dam management strategies for biodiversity conservation.