The photosynthetic ciliate Mesodinium rubrum is a common member of coastal phytoplankton communities that is well adapted to low-light, turbid ecosystems. It supports the growth of or competes with harmful dinoflagellate species for cryptophyte prey, as well as being a trophic link to copepods and larval fish. We have compiled data from various sources (n = 1063), on the abundance and distribution of M. rubrum in Chesapeake Bay and its tributaries. Because M. rubrum relies on obtaining
organelles from cryptophyte algae to maintain rapid growth, we also enumerated cryptophyte algae in the portion of these samples that we collected (n = 386). M. rubrum occurred in oligohaline to polyhaline regions of Chesapeake Bay and throughout the year. Blooms (>100 cells ml-1) of M. rubrum primarily occurred during spring, followed by autumn. When compared across all seasons, M. rubrum abundance was positively correlated to temperature and cryptophytes, and negatively correlated with salinity. However, more focused analyses revealed that M. rubrum abundance during spring was associated with surface layer warming and decreased salinity, while early autumn assemblages were associated with surface cooling. These results imply there are distinct seasonal niches for M. rubrum blooms. Blooms of M. rubrum were more common in tributaries than in the main stem Bay and tended to be restricted to salinities under 10 PSU. Despite the rarity of “red water” events, M. rubrum is a ubiquitous mixotroph in Chesapeake Bay and at times likely exerts a strong influence on cryptophyte algal abundance and hence planktonic food web structure.