Habitat degradation is expected to alter community structure and consequently, ecosystem functions including the maintenance of biodiversity. Understanding the underlying abiotic and biotic assembly mechanisms controlling temporal and spatial community structure and patterns is a central issue in biodiversity conservation. In this study, using monthly time series of fish abundance data collected over a three-year period, we compared the temporal community dynamics in natural habitats and poplar plantations in one of the largest river-lake floodplain ecosystems in China, the Dongting Lake. We found a prevailing strong positive species covariance, i.e. species abundance changes in the same way, in all communities that was significantly negatively impacted by higher water nutrient levels. In contrast to species covariance, community stability, which was measured by the average of aggregated abundance divided by temporal standard deviation, was significantly higher in poplar plantations than in natural habitats. The positive species covariance, which was consistent for both wet and dry years and among habitat types, had significantly negative effects on community stability. Furthermore, our results demonstrated that the ecological stochasticity (i.e. community assembly processes generating diversity patterns that are indistinguishable from random chance) was significantly higher in natural sites than in poplar plantations, suggesting that deterministic processes might control the community composition (richness and abundance) at the modified habitat through reducing species synchrony and positive species covariance observed in the natural habitats, leading to significantly lower temporal β-diversity. When combined, our results suggest that habitat modification created environmental conditions for the development of stable fish community in the highly dynamic floodplains, leading to niche-based community with lower temporal β-diversity.