A time series of relative abundance of Atlantic menhaden Brevoortia tyrannus was compared with concomitant time series of phytoplankton and zooplankton abundance in the York River, Virginia. Menhaden catch-per-unit-effort (CPUE) was measured from pound net catches and disaggregated by fish size. Phytoplankton and zooplankton were enumerated and assigned to general taxonomic categories from collection stations in proximity to the pound nets. The CPUE data were divided into juvenile and adult categories and segmented over time based on transition points in the time series identified using sequential t test analysis of regime shifts (STARS). Transitions in adult CPUE were more closely associated with transitions in zooplankton abundance than with changes in phytoplankton abundance. The data suggest that menhaden adjust their mesoscale distributions within a large estuarine system like Chesapeake Bay based on changing patterns of zooplankton prey and independently of phytoplankton blooms. This distribution preference is attributed to the efficiency in which the fish filter various sizes of particles from the water column. The exception to this trend occurred in late summer when menhaden abundance declined in the York River despite the high abundance of suitable prey. This was likely the result of a bloom of the ichthyotoxic dinoflagellate Cochlodinium polykrikoides, which maintained densities known to be lethal to fish for 1 month. Collectively, these results suggest that adult menhaden play a minimal role in providing ecosystem filtration and may actually promote primary production through the removal of zooplankton grazers and the excretion of nutrients.