Aquatic ecosystems face mounting threats from climate warming and persistent pollutants like per- and polyfluoroalkyl substances (PFAS). Conventional risk assessments based on single-chemical exposure and species sensitivity distributions (SSDs) overlook ecological complexity. Here, we present a network-based framework to assess ecosystem health under PFAS (10 μg/L, an SSD-defined safe level) and warming (+3.0 °C) using mesocosm experiments. PFAS altered carbon source use in top consumers and reduced energy transfer to higher trophic levels, while warming narrowed niche space and intensified competition. Combined stressors partially offset PFAS effects but disrupted overall trophic structure. All treatments induced an unstable "inverted triangle" trophic configuration in plankton communities. We identify keystone taxa (e.g., Nicholsicypris normalis) and sensitive species (e.g., ciliates) that regulate stability via trophic cascades, using biomass loss, niche contraction, energy flow shifts, and network connectivity. Based on these, we develop a novel Ecological Health Quality Index (EHQI), integrating trophic topology and interaction strength shaped by sensitive species. EHQI declined from 41.83 (healthy) to 22.51 under PFAS and to 21.51 under combined stress. Our approach advances ecosystem assessment by emphasizing sensitive species and trophic stability, enabling early warning detection in aquatic ecosystems under complex stressors.
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