Keywords:San Francisco Estuary primary production phytoplankton carbon ammonium nitrate a b s t r a c tWe describe the results of a series of 96-h enclosure experiments conducted using water from stations in the northern San Francisco Estuary (SFE) along a gradient in ammonium (NH 4 ) and nitrate (NO 3 ) concentrations. Using dual-labeled 13 C/ 15 N tracers, we followed the timing and sequence of primary (carbon, C) production and phytoplankton nitrogen (N) use during experimental phytoplankton blooms. Our results show that diatoms consistently drive the phytoplankton blooms in the enclosures. By tracing both C and N uptake we provide clear evidence that high rates of C uptake are linked to phytoplankton NO 3 , and not NH 4 , use. Results from kinetics experiments demonstrated higher specific uptake rates (V MAx ) for NO 3 compared to NH 4 in the SFE. Finally, dissolved inorganic carbon and nutrient drawdown ratios in the enclosures from the chronically high NH 4 regions of the SFE were substantially lower than predicted from the Redfield ratio, suggesting suppressed C uptake, in relation to other elemental uptake. Our conceptual model of the DIN interactions that lead to higher primary production and phytoplankton blooms in the SFE suggests that higher rates of primary production that accompany phytoplankton NO 3 uptake are sufficient to outpace phytoplankton losses, leading to blooms, compared to the lower rates associated with NH 4 uptake (only 20% of that based upon NO 3 ). Historical changes in wastewater practices have increased the proportion of NH 4 to the DIN pool in the SFE leading to reduced access to NO 3 by phytoplankton. This may help to explain some of the reduced primary production and phytoplankton biomass observed there since the 1970s.