The autotrophic plankton assemblage along the subtropical coastal embayments of the South Brazil Bight is dominated by the cyanobacterium Synechococcus. This investigation aims to assess its contribution to the total carbon metabolism within the planktonic system of Mamanguá Ría, a subsystem of the Bay of Ilha Grande, southeast Brazilian coast. We hypothesized that photosynthetic carbon fixation by cyanobacteria does not support the plankton metabolism inside the Ría. Net community production (NCP) was calculated from differences between gross community production (GCP) and dark community respiration rates measured by in situ incubations using the oxygen light-and-dark technique. Our results reveal the carbon budget inside the Ría is not balanced by autotrophic production. The deficit of net ecosystem production throughout the year ranged from 0.5 to 1.5 mg m −2 d −1 below what is necessary to sustain local plankton metabolism. We argue that the offset between daily GCP and total community respiration may be balanced by grazing of nano-heterotrophs on heterotrophic bacteria. Our conclusions apply to the majority of the meso-oligotrophic Brazilian inner shelf waters away from estuarine plumes and upwelling systems.