Ciliate abundance and biomass were determined at three anchored stations in the Han River estuary trimonthly from May 2006 to February 2008. The total abundance of ciliates ranged from 0-13,853 cells $l^{-1}$ and biomass ranged from $0.00-73.98;ugC;l^{-1}$. Owing to the large seasonal temperature variation (range 0.20-$27.2^{circ}C$), ciliate abundance displayed marked seasonal variation, being higher in summer than in other seasons. Tintinnids dominated the ciliate communities at station YC where suspended sediment was highest. Difference of ciliate biomass between ebb tide and flood tide were irregular. Seasonal variations of ciliate carbon biomass at each station were related to temperature, suspended sediment and chl.a, especially nano chl.a. Geographical variations of ciliate carbon biomass in each season were related to suspended sediment and salinity.