Aquatic eukaryotic communities play important roles in biogeochemical nutrient cycling and ecosystem functioning and are also sensitive to changes in aquatic environmental conditions. Qianmudang Reservoir is a typical shallow drinking-water reservoir supplying approximately 500,000 residents in Haiyan County, Zhejiang Province, China. However, the seasonal dynamics of its aquatic eukaryotic communities remain poorly understood. In the present study, we used 18S rRNA gene amplicon sequencing to characterize aquatic eukaryotic communities across four seasonal surveys in 2025. A total of 4903 eukaryotic amplicon sequence variants (ASVs) were obtained. ASV richness and Shannon diversity were highest in summer. Cryptomonas (Cryptophyta) showed the highest overall relative sequence abundance at the genus level, TSAR accounted for the greatest relative sequence abundance at the supergroup level. Community composition showed pronounced seasonal differentiation, and indicator value analysis identified 17 season-associated genera. Only 33 ASVs were detected across all four seasons, and β-diversity partitioning revealed that seasonal community dissimilarity was dominated by ASV turnover rather than nestedness-resultant differences. Partial db-RDA identified associations between community composition and total phosphorus, dissolved oxygen and water temperature, where total phosphorus had the strongest marginal effect. Variation partitioning further showed that environmental variables and sampling period jointly explained a large proportion of community variation. These findings revealed pronounced seasonal restructuring of aquatic eukaryotic communities at both taxonomic and ASV levels and highlight the importance of ASV turnover and occupancy patterns for understanding temporal biodiversity dynamics in shallow drinking-water reservoirs.