Planktonic ciliate composition, abundance and its response to environmental change were investigated during four seasons (winter of 2013, spring, summer and autumn of 2014) in Daya Bay, the South China Sea. A total of 41 species belonging to eight orders were identified, 14 of which were dominant. Planktonic ciliate communities showed a distinct seasonal pattern in ciliate abundance and a clear seasonal shift in the taxonomic composition. The largest number of ciliate species occurred in summer, whereas the highest abundance peaked in spring, mainly due to oligotrichids. In terms of spatial distribution, ciliate species were abundant in the area of artificial reefs, and ciliate abundance was higher in the Dapeng Cove aquaculture area and lower at the Daya Bay Nuclear Power Station. Clustering analysis demonstrated that the seasonal variations of the ciliate community structure were more obvious than spatial variations. Multivariate and univariate analyses illustrated that ciliate abundance was significantly correlated with the water nutrient level and chlorophyll-a concentration, temperature, salinity and dissolved oxygen. Moreover, the dominant abiotic environmental factors affecting the spatial pattern of ciliate communities varied between seasons.