Evaluation of photosynthetic competency in time and space is critical for better estimates and models of oceanic primary productivity. This is especially true for areas where the lack of iron (Fe) limits phytoplankton productivity, such as the Southern Ocean. Assessment of photosynthetic competency on large scales remains challenging, but phytoplankton chlorophyll a fluorescence (ChlF) is a signal that holds promise in this respect as it is affected by, and consequently provides information about, the photosynthetic efficiency of the organism. A second process affecting the ChlF signal is heat dissipation of absorbed light energy, referred to as non-photochemical quenching (NPQ). NPQ is triggered when excess energy is absorbed, i.e. when more light is absorbed than can be used directly for photosynthetic carbon fixation. The effect of NPQ on the ChlF signal complicates its interpretation in terms of photosynthetic efficiency, and therefore most approaches relating ChlF parameters to photosynthetic efficiency seek to minimize the influence of NPQ by working under conditions of sub-saturating irradiance. Here, we propose that NPQ itself holds potential as an easily acquired optical signal indicative of phytoplankton physiological state with respect to Fe limitation. We present data from a research voyage to the Subantarctic Zone south of Australia. Incubation experiments confirmed that resident phytoplankton were Fe-limited, as the maximum quantum yield of primary photochemistry, F-v/F-m, measured with a fast repetition rate fluorometer (FRRf), increased significantly with Fe addition. The NPQ "capacity" of the phytoplankton also showed sensitivity to Fe addition, decreasing with increased Fe availability, confirming previous work. The fortuitous presence of a remnant warm-core eddy in the vicinity of the study area allowed comparison of fluorescence behaviour between two distinct water masses, with the colder water showing significantly lower F-v/F-m than the warmer eddy waters, suggesting a difference in Fe limitation status between the two water masses. Again, NPQ capacity measured with the FRRf mirrored the behaviour observed in F-v/F-m, decreasing as F-v/F-m increased in the warmer water mass. We also analysed the diel quenching of underway fluorescence measured with a standard fluorometer, such as is frequently used to monitor ambient chlorophyll a concentrations, and found a significant difference in behaviour between the two water masses. This difference was quantified by defining an NPQ parameter akin to the Stern-Volmer parameterization of NPQ, exploiting the fluorescence quenching induced by diel fluctuations in incident irradiance. We propose that monitoring of this novel NPQ parameter may enable assessment of phytoplankton physiological status (related to Fe availability) based on measurements made with standard fluorometers, as ubiquitously used on moorings, ships, floats and gliders.