Natural- and human-induced environmental changes lead to structure shifts in phytoplankton communities, impacting the resilience, functioning, and ecosystem services of lakes. Given the scarcity of long-term monitoring data, particularly in the tropical region, our understanding of phytoplankton communities (cyanobacteria and eukaryotic micro-algae) and their triggering factors remains limited over decadal scales. We determined whether shifts in phytoplankton community within Huguangyan Maar Lake, a tropical lake, are linked to climate warming and assessed whether the observed changes resemble those documented in temperate or arctic regions. We applied 23S rRNA gene metabarcoding to 43 sediment samples covering the past ∼140 years, and explored how the phytoplankton community respond to multiple environmental stresses. Phytoplankton diversity exhibited a marked increase beginning in the 1940s, followed by a distinct decline in the 1980s. Notably, a significant shift in community composition emerged toward the late 1980s, characterized by a rise in the relative abundance of diatoms (Aulacoseiraceae) and a concurrent decrease in rhodophytes (Bangiaceae) and cyanobacteria (Synechococcaceae). This pattern contrasted sharply with trends observed in other lakes, where cyanobacteria have maintained dominance in recent decades.Through integrated application of Mantel tests and random forest multivariate modeling, nutrient loading emerged as the predominant driver of community restructuring outweighing climatic factors. Concurrently, anthropogenic combustion signatures, such as polycyclic aromatic hydrocarbons, demonstrated significant covariance with phytoplankton assemblage reconstructing. This study highlights the dual impact of anthropogenic nutrients input and pollutants on phytoplankton communities in tropical lakes and provides important implication for future pollution and nutrient control.
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