Better understanding of many aspects of plankton ecology requires long term, high frequency observations of community structure, which traditional sampling techniques cannot provide. To meet this challenge, we have developed a series of automated submersible flow cytometers for analysis of phytoplankton. The newest development, Imaging FlowCytobot, includes cell imaging capabilities for microplankton. When combined with automated image analysis and classification, this instrument provides unprecedented time series of community structure with taxonomic resolution (often to genus or even species level). Like its predecessors, Imaging FlowCytobot carries out automated standard analysis and anti-fouling procedures, and it has proven capable of 6-month uninterrupted deployment at the Marthaâs Vineyard Coastal Observatory, a cabled facility on the New England shelf. We document these capabilities with detailed observations of wintertime diatom blooms measured in 2007. The bloom dynamics are complex with multiple event-scale fluctuations in diatom abundance and taxonomic composition over several months. Shifts in dominant genus are evident as the season progresses. Multi-year time series of this type will be the key to understanding the regulation of these fluctuations and their response to environmental change.