This study investigates whether environmental stress alters the mechanisms by which biodiversity sustains ecosystem functioning and stability. To address this question, we established 48 freshwater mesocosms with submerged macrophyte communities and exposed them to two stressors: warming and pulsed surface runoff pollution. Results show that warming significantly increased the net biodiversity effect (NBE), whereas runoff pollution had no significant impact on functioning or its components. Complementarity effects remained the primary mechanism driving ecosystem functioning, with their positive relationship to functioning being unaffected by either stressor. Selection effects played a similarly important role in driving ecosystem functioning, but their correlation with functioning showed a weakening trend under pollution. Regarding stability, warming maintained overall ecosystem stability by reducing species asynchrony while simultaneously increasing average species stability, without altering the positive relationships between overall stability and these two components. Further analysis revealed that average species stability contributed more strongly to overall stability than species asynchrony, highlighting the dominant role of key species in stability maintenance. Path analysis indicated that warming indirectly buffered its potential negative effects on stability primarily by enhancing ecosystem functioning. While pollution induced a certain degree of species asynchrony, this positive regulatory effect was overridden by the pronounced biomass dominance of key species within the experimental scale. Overall, these findings suggest that the mechanisms by which biodiversity maintains ecosystem functioning and stability may shift under environmental stress, although these mechanisms still exhibited strong robustness under relatively moderate stress intensities. This study advances the understanding of how freshwater ecosystems respond to global change in terms of functioning and stability mechanisms, and provides a theoretical basis for ecosystem management and ecological risk assessment.