The estuarine turbidity maximum (ETM) is a zone of elevated organic matter concentrations and it is an important habitat for bacteria, zooplankton, and early-life-stages of fish. In an effort to identify the key mechanisms controlling production, we measured plankton community metabolism on a series of high-resolution spatial surveys in the upper Chesapeake Bay. The spatial patterns of metabolism revealed the highest primary production and community respiration rates downstream of the ETM region, and net heterotrophy in winter and spring. Also, strong correlations between plankton community metabolism and phytoplankton pigment concentrations, including chlorophyll-a and dinoflagellate indicating pigment peridinin, were observed. These correlations suggest that mixotrophic dinoflagellates were key organisms linking detrital and algal organic matter to higher trophic levels. It is hypothesized that the physiological advantages of mixotrophic dinoflagellates (i.e., autotrophic, heterotrophic) combined with the physical conditions in the ETM which enhance the quantity and quality of organic matter give rise to the high secondary production in the upper Chesapeake Bay.