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Lake nutrient budgets and hydrology are being altered by human activities and climate change, yet little is known of how fertilization and hydrologic mechanisms interact to structure assemblages of primary producers. Here, we present sediment records from a large shallow lake in Southwest China to separate the relative importance of nutrients and hydrological fluctuation in regulating the abundance and composition of primary producers during the twentieth century, with a focus on their differential effects on diatoms and cyanobacteria. Shifts in sedimentary particle-size distribution were consistent with the documented events of hydrological regulation during similar to 1953-1971 and subsequent changes in water level associated with severe droughts. Nutrient enrichment since similar to 1965 resulted in a significant increase in the abundance of total phototrophs (pheophytin a, -carotene) as inferred from pigment analyses, with stronger responses of cyanobacteria (echinenone, zeaxanthin) over siliceous algae (diatoxanthin). Fossil diatom assemblages revealed a pronounced replacement of benthic taxa by eutrophic and planktonic species (e.g., Fragilaria crotonensis) since similar to 1973, but we observed a significant increase of small benthic Fragilaria sensu lato taxa following similar to 2005, which generally corresponded with a moderate increase in fossil pigments. Although eutrophication was the paramount predictor of changes in phototrophs during the last century, variation in lake hydrology due to climate and water management also modulated phototroph abundances and, more recently, diatom assemblages. Specifically, our sediment evidence suggests that hydrological fluctuation has overridden fertilization by nutrients in structuring diatom composition, leading to a heterogeneous response of cyanobacteria and diatoms to external forcing of this shallow lake.