The northern San Francisco Estuary (nSFE) is an urban estuary supplied with anthropogenic nutrient inputs, yet spring blooms are uncommon and phytoplankton biomass is low. The low levels of chlorophyll (<5 µg L−1) have likely contributed to declines in several native fishes, and there is a need to evaluate the conditions that could allow for increased phytoplankton. Increased ammonium (NH4) loads have been hypothesized to modulate the magnitude of blooms in nSFE (the “NH4 hypothesis”) as a result of inhibition of phytoplankton NO3 uptake that limits access to the greater nitrogen (N) pool of nitrate (NO3). This hypothesis, tested in enclosures, but not in the field until now, is that lack of access to NO3 limits primary production and consequently the accumulation of chlorophyll. Here, we test this in the field with the following aims: (1) to observe the uptake response of phytoplankton in different flow and N loading conditions, (2) determine whether the sequence of uptake rates suggested by the “NH4 hypothesis” occurs and (3) obtain depth-integrated nutrient uptake rates to better constrain published criteria for bloom formation. Weekly measurements of NH4 and NO3 uptake, and primary production rates were made during spring 2011–2012, along with nutrient and chlorophyll concentrations during two contrasting hydrological conditions of high vs low freshwater flow. In conditions with high freshwater flow (maximum of 2405 m3 s−1), there were lower nutrient concentrations than with low/normal flows (e.g., NO3 of 10 µmol L−1 compared to 30 µmol L−1), with low N uptake and primary production rates. With low flow (maximum of 1304 m3 s−1), there was elevated chlorophyll and blooms occurred, especially in shallow well-lit shoals where chlorophyll reached 60 µg L−1. The higher levels of chlorophyll and primary productivity resulted from uptake of ambient NO3 by phytoplankton, and f-ratios >0.5. This was enabled by phytoplankton uptake of NH4 to below inhibitory levels, as proposed by the “NH4 hypothesis.” The depth-integrated uptake rate data were used to refine a model that yields flow and nutrient concentration criteria necessary for bloom formation and confirmed that washout flows were the most useful predictor of blooms. Understanding the interaction of phytoplankton biomass with nutrient variability requires evaluating changes in C and N uptake rates and river flow. These dynamic changes are central to understanding why some urban estuaries have lower productivity than expected, and would be difficult to evaluate using biomass data alone. This study points to the importance of treating inorganic N separately as NH4 and NO3 rather than lumping together as DIN and to use rate process data as a mechanistic way to understand, predict and minimize cultural eutrophication impacts.