To examine factors regulating the summer population dynamics of tintinnid species, temporally high-frequency observations of tintinnid ciliates were performed in Hiroura Estuary in Sendai Bay. Sampling was conducted on alternate days from 5 July to 2 August, 2010 at three estuary sites to examine which environmental (water temperature, salinity and tidal level change) and biological (abundances of Chl-a, bacteria, protozoans and zooplankton) factors are important for determining temporal changes in abundance and apparent population change rates for tintinnid species. During the study period, 20 tintinnid species were found and showed drastic population changes within a few days, resulting in different tintinnid assemblages from the first to the second half of the study period. Multivariate analysis and generalised linear mixed models showed that several environmental and biological factors were related significantly with the abundance and apparent population change rate of each tintinnid species, but no effect of potential predators such as copepods was found for the abundance and change rate. These results suggest that physicochemical and food conditions play more important roles than predation pressure in short-term temporal changes of tintinnid populations during summer in estuary environments.