We compare primary productivity estimates based on different photosynthetic ‘currencies’ (electrons, O<sub>2</sub> and carbon) collected from the dynamic coastal upwelling waters of the California Current. Fast Repetition Rate Fluorometry and O<sub>2</sub>/N<sub>2</sub> measurements were used to collect high-resolution underway estimates of photosynthetic electron transport rates and net community productivity, respectively, alongside on-station <sup>14</sup>C uptake experiments to measure gross carbon fixation rates. Our survey captured two upwelling filaments at Cape Blanco and Cape Mendocino with distinct biogeochemical signatures and iron availabilities, enabling us to examine photosynthetic processes along a natural iron gradient. Significant differences in photo-physiology, cell sizes, Si:NO<sub>3</sub><sup>-</sup> draw-down ratios, and molecular markers of Fe-stress indicated that phytoplankton assemblages near Cape Mendocino were Fe-stressed, while those near Cape Blanco were Fe-replete. Upwelling of O<sub>2</sub>-poor deep water to the surface complicated O<sub>2</sub>-based net community productivity estimates, but we were able to correct for these vertical mixing effects using continuous [N<sub>2</sub>O] surface measurements and depth-profiles of <span style="border-bottom: 1px solid #000; vertical-align: 50%; font-size: .7em; color: #000;">∂[O<sub>2</sub>]</span><span style="margin-left: -2.5em; margin-right: .5em; vertical-align: -15%; font-size: .7em; color: #000;">∂[N<sub>2</sub>O]</span>. Vertical mixing corrections were strongly correlated to sea surface temperature, which serves as an N<sub>2</sub>O-independent proxy for upwelling. Following vertical mixing corrections, all three productivity estimates reflected trends in Fe-stress physiology, indicating greater productivity near Cape Blanco compared to Cape Mendocino. For all assemblages, carbon fixation varied as a hyperbolic function of electron transport rates, but the derived parameters of this relationship were highly variable and significantly correlated with physiological indicators of Fe-stress (σ<em><sub>PSII</sub></em>, F<sub>V</sub>/F<sub>M</sub>, Si:NO<sub>3</sub><sup>-</sup> and diatom-specific PSI gene expression), suggesting that iron availability influenced the coupling between photosynthetic electron transport and subsequent carbon fixation. Net community productivity showed strong coherence with daily-integrated photosynthetic electron transport rates across the entire cruise track, with no apparent relationship with Fe-stress. This result suggests that fluorescence-based estimates of gross photochemistry are still a good indicator for bulk primary productivity, even if Fe-limitation influences the stoichiometric relationship between productivity currencies.