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Climate change is likely to stimulate variations in phytoplankton composition and production in gradually eutrophicating water, with negative consequences for the water quality of many reservoirs. This study analyzed the effects of climate warming and increased nutrient loading on algae communities recorded by sedimentary pigments in the Changtan Reservoir of southeastern China from 1985 to 2015. Pigment profiles indicated that cyanobacteria, green algae, diatoms, and cryptophytes were the dominant algae groups during the study period. Algae biomass increased significantly after 2007, correlated (by the Mann-Kendall test) with an upswing in nutrient load and rising air temperatures. Generalized additive model (GAM) analysis demonstrated that total phosphorous was the dominant contributor to algae biomass during the study period, accounting for 41.37%, 43.86%, 58.91%, 97.36%, and 70.24% of variations in total algae, cyanobacteria, green algae, diatom, and cryptophyte biomass, respectively. The relative contributions of annual average air temperature to variations in total algae, cyanobacteria, green algae, diatom, and cryptophyte biomass were 10.80%, 14.02%, 14.13%, 24.64%, and 17.31%, respectively, depending strongly on nutrient load. In conclusion, climate warming and increasing anthropogenic nutrient loading forced phytoplankton dynamics and drove increasing algae biomass in this reservoir, suggesting that future water quality management practices should consider both meteorological and anthropogenic factors affecting algae communities.