Ciliate, heterotrophic microflagellate (hflag) and autotrophic microflagellate (aflag) abundances are reported for mesohaline Chesapeake Bay waters based on samples gathered from April through October 1985-1987. Total water column averages for ciliate and microflagellate abundances were typical of eutrophic marine systems. Ciliate density ranged from 17·2 cells ml-1 in April to 1·8 cells ml-1 in September; hflag ranged from 3·7 × 103 cells ml-1 in June to 1·1 × 103 cells ml-1 in October. In spring the majority of ciliate and hflag standing stocks (70% and 64%, respectively) were located in bottom and transition waters; during summer months the majority (approximately 85% of both groups) were in surface and transition waters. During fall, ciliate stock was concentrated (72%) in surface waters and hflag were relatively evenly distributed in the three water column zones. Ciliate and microflagellate numbers were not directly related to chlorphyll α concentration except in the bottom layer, where simultaneous declines accompanied anoxia. Ciliate concentrations correlated with total numbers of microflagellates and hflag abundance, but not aflag density. We discuss the relative importance of predation and food availability in regulating ciliate and hflag concentrations in mesohaline Chesapeake Bay waters. © 1990.