Plankton (including phytoplankton and zooplankton) play a crucial role in maintaining aquatic ecosystem stability, yet their influence on the stability of fragile freshwater ecosystems in arid regions remains underexplored. This study systematically investigated the biodiversity dynamics, co-occurrence patterns and community stability of plankton in common freshwater bodies (rivers and reservoirs) within the Yanhe River Basin, a representative arid region in northern China. The response thresholds of plankton communities to key influencing factors were determined. The results indicated greater diversity and similarity among riverine plankton communities in the main stream and tributaries, despite lower biomass compared to those in reservoirs. Plankton network robustness and community stability were also higher in rivers than in reservoirs, mainly due to distinct roles of phytoplankton and zooplankton diversity across different types of water bodies. Water nutrients (e.g., nitrogen sources), pH, turbidity and the ratio of zooplankton to phytoplankton biomass (Z/P ratio) emerged as key factors shaping plankton community structure and stability. The threshold ranges of total nitrogen, pH, turbidity and Z/P ratio for plankton community responses were 0.053 to 1.126 mg/L, 8.7 to 9.0, 28.53 to 83.23 NTU, and 0.64% to 16.0%, respectively. This study provides a glimpse into how plankton diversity and community interactions drive freshwater ecosystem stability, and proposes operational guidelines for water resource management and ecological conservation under arid conditions.