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Reconstructing Holocene vegetation history and human impact on vegetation is critical for understanding past interactions between humans and nature. This study concentrates on the lower West River area in Southern China, offering high-resolution reconstructions of vegetation changes over the last 9000 years. Our findings reveal that during the Holocene Climatic Optimum (9–5 ka BP), the area was predominantly covered by dense evergreen broad-leaved forests. Around 5.1 ka BP, the emergence of marsh forests, as evidenced by abundant pollen of Glyptostrobus and in situ buried woods and roots, indicated a transition towards a wetland ecosystem. Notably, a thriving wetland environment and high production of peat deposits dating from 4.3 ka to 2.5 ka BP reflect the continuous drop of lake levels and the formation of swamps driven by a climatic pattern marked by decreased precipitation, potentially linked to a reduction in summer monsoon intensity during the latter part of the Holocene. This period of wetland expansion also coincides with the earliest evidence of rice cultivation in Southern China, suggesting a relationship between agricultural development and regional landscape changes. Additionally, millennial-scale paleo-megafloods are not only identified by lithological features but also by pollen taxa and principal component analysis. Despite the temporary disruptions of the marsh forest, it demonstrated resilience, quickly recovering within decades. By approximately 2.5 ka BP, a significant increase in rice-type Poaceae pollen and Pteridophyte spores, alongside the sharp decline of Glyptostrobus and a decrease in arboreal taxa, were observed. This shift in pollen spectra, coupled with a PC1 curve of principal component analysis, points to intensified human activity as a primary driver behind the collapse of the local wetland ecosystem. These findings align with regional evidence from the Pearl River Delta and coastal Southern China, highlighting extensive human intervention in natural forests and the onset of large-scale agriculture post-2.5 ka BP. [ABSTRACT FROM AUTHOR]