Microzooplankton are thought to play important roles in grazing and nutrient recycling in coastal waters, but relatively little is known about their patterns of natural variability. To address this gap for the New England inner shelf, we examined ciliate images collected during three years (2006-2009) of Imaging FlowCytobot deployments at the Marthas Vineyard Coastal Observatory. Imaging FlowCytobot records images of cells with chlorophyll fluorescence above a trigger threshold, so analysis focused on mixotrophic and herbivorous ciliates. Images were categorized as Myrionecta rubra, Laboea strobila, and a mixture of mainly strombidid ciliates; tintinnids were also detected, but with low efficiency probably due to their low chlorophyll fluorescence. Total ciliate abundance did not show distinct seasonality, but for both M. rubra and L. strobila abundances were lowest in early summer with intermittent peaks lasting weeks to months at other times of year. Timing of these peaks was relatively consistent for L. strobila (late spring and early fall), but varied each year for M. rubra. Average ciliate size was largest in spring and fall and lowest in summer, possibly in response to seasonality in the phytoplankton community where picoplankton and small nanoplankton dominate in summer. Larger cell sizes dominated the M. rubra population in winter, but not in a simple association with nutrient concentration as has been previously suggested. Preliminary results suggest seasonality in temperature may play a role in regulating M. rubra size.