Primary and bacterial productivity (PP and BP, respectively) were measured in the lower Itajaí-Açu estuary and in the adjacent shelf, under low river discharge conditions. The experiment was carried out in April, 2000, when physical, chemical and biological variables were recorded in five stations: three in the estuary and two in the inner shelf. Salinity, temperature, turbidity and light intensity were determined in vertical profiles; dissolved oxygen, nutrients, chlorophyll-a, primary (PP) and bacterial production (BP) were sampled at surface and near the bottom. The BP ranged from 0.5 to 11.3 mg C.m-3 .h-1 , and the highest values were recorded at the inner stations of the estuary, associated with lower salinity and light intensity and higher dissolved nutrients concentration. On the other hand, PP was higher in the inner shelf, with PP increasing from 2.0 to 30 mg C.m-3 .h-1 . The phytoplankton biomass showed the same trend, increasing from 0.2 to 8.4 µg/L at the surface. The PP was limited by light in the inner estuary and by the PO4 concentration in the inner shelf. The higher productivity zone was formed in front of the estuarine mouth, as expected, since water transparency increases leading the consumption of the rich-nutrient waters from the estuary by autotrophic organisms. The data indicated that the ecosystem metabolism shift from heterotrophic to autotrophic in a very small length scale (few kilometers) during the sampled conditions.