Diversity of fishes in karst Plateau lakes, Guizhou, China

• Marked spatial heterogeneity in fish community assembly across karst plateau lakes. • Contrasting assembly processes: Stochasticity dominates in Baihua and Wanfeng Lakes, determinism in Hongfeng Lake. • Water quality indirectly shapes assembly via modulating network stability. • Novel integration of eDNA, network analysis, and SEM for community ecology. Exploring fish community structure and assembly mechanisms across multiple ecological scales is crucial for understanding the sustainable management of lake ecosystems. This study focused on a typical karst plateau lake in Southwest China, including Baihua Lake, Hongfeng Lake and Wanfeng Lake. integrating eDNA high-throughput sequencing, network topology analysis, and structural equation modeling to systematically analyze the spatial patterns, assembly processes, and environmental responses of the fish community. The results demonstrate that fish species diversity exhibits significant spatial heterogeneity. Multiple lines of evidence, including the neutral model, ecological niche width, and βNTI collectively indicate that stochastic processes predominantly govern the assembly of fish communities, particularly in Baihua Lake and Wanfeng Lake. In contrast, deterministic factors such as environmental filtering and spatial constraints play a more prominent role in Hongfeng Lake. Analyses of distance decay and environmental factors further reveal that the relationship between community similarity, geographical distance, and environmental heterogeneity varies significantly across regions. Molecular ecological network analysis reveals that Hongfeng Lake exhibits the largest network scale and highest stability, which supports the maintenance of biodiversity. The structural equation model demonstrates that water quality directly influences community assembly by regulating the molecular ecological network, while assembly exerts a negative regulatory effect on network stability. The overall model shows a high goodness-of-fit (GoF = 0.74), and core path relationships were statistically significant. This study elucidates the multidimensional assembly mechanisms of fish communities in karst lakes and the regulatory interactions within the network, providing novel insights and a theoretical foundation for the management and restoration of biodiversity in high-altitude lake ecosystems.