Over a diurnal cycle, light energy varies between extremes of darkness and abundance causing diurnal fluctuations in light harvesting capabilities of phytoplankton and photosynthetic rate processes that can eventually result in changes in C export, dissolved organic matter composition, nutrient cycling and ecosystem function. However measuring primary production using conventional bottle incubations with labeled carbon is extremely labor intensive and inadequate to provide the time and space resolution required to monitor changes in phytoplankton physiology and carbon fixation rates from changing incident irradiance levels over the course of the day and over large areas. In this study, we use variable chlorophyll fluorescence, which allowed us to measure phytoplankton photosynthetic physiology instantaneously and over the entire diurnal cycle. These measurements were conducted over the biogeochemically complex waters around the Korean Peninsula. We show how phytoplankton make diurnal adjustments to their photosynthetic light use efficiency and upregulate non-photochemical quenching (NPQ) or heat dissipation of excess energy during midday. These results are discussed in the context of various 1) phytoplankton functional groups, 2) their great relevance for models of marine primary productivity that continue to suffer from inadequate shipboard estimates of phytoplankton photosynthetic quantum yields, and 3) their importance for deriving marine primary productivity from current and future geostationary ocean color sensors.