A reduction in predator-induced grazing pressure may be a mechanism that facilitates the formation and persistence of harmful algal blooms. Here, the hypothesis was tested that the heterotrophic ciliate Favella ehrenbergii would use avoidance behaviors to reduce encounters with the toxic bloom-forming alga, Heterosigma akashiwo. Using video and image-analysis, population distributions and three-dimensional movements of F. ehrenbergii and H. akashiwo were quantified in triplicate, hourly for 11 h, at nine horizons in a 1-liter experimental column. The salinity structure in the column was manipulated to include a halocline, resulting in layer formation by H. akashiwo. The ciliate's vertical distributions were restricted to high-salinity waters below the halocline, while H. akashiwo was broadly halo-tolerant and could occupy the whole water column. When observed together, F. ehrenbergii did not avoid layers of H. akashiwo. In the presence of H. akashiwo, F. ehrenbergii mortality rates were higher than in either no prey or beneficial prey controls. Swimming behaviors of F. ehrenbergii were erratic, in response to H. akashiwo, compared to aggregative movements in response to beneficial prey, indicating either a behavioral response or the effect of H. akashiwo toxicity on the ciliate. The inability of F. ehrenbergii to avoid H. akashiwo enhanced predator mortality and may contribute to the survival of the harmful algal bloom species, ultimately promoting the formation of H. akashiwo harmful algal blooms.