Abstract: To explore the structural characteristics of planktonic prokaryote communities and their correlation with environmental factors, a survey of planktonic prokaryotes in the Maling River was conducted during the wet seasons and dry seasons using environmental DNA technology and diversity index analysis. Redundancy analysis was used to explore the relationship between prokaryotic diversity in the Maling River and environmental factors. The results showed that planktonic prokaryotes belonged to 28 phyla and 377 genera in the wet season, planktonic prokaryotes belonged to 18 phyla and 248 genera in the dry season, and the dominant species were Actinobacteria, Proteobacteria and Bacteroidetes. A comparison of the community structure characteristics between seasons indicated that the species richness of the planktonic prokaryotes community in the wet season was significantly higher than that in the dry season. However, there was no significant difference in the diversity index and evenness index of the planktonic prokaryotes community in the wet and dry seasons. The pH, total nitrogen, dissolved oxygen, ammonia nitrogen and conductivity were the key environmental factors affecting the changes of the planktonic prokaryotes community in the Maling River. Although the species composition changed with the seasons, the overall community structure exhibited considerable stability, and the ecosystem could maintain a balanced state during seasonal changes. This fully demonstrated the adaptive resilience characteristics of karst landform and river ecosystems.