A physical and bio-optical field survey of the Monterey Bay area was conducted during May–June 2008. The combined bio-optical and physical data may be summarized as a transition between two end-member states during the late spring to summer upwelling season: (1) the mesotrophic, nanoflagellate-dominated, low-salinity surface waters (chlorophyll-a ∼ 0.5–2 mg m−3; S < 33.4) of the California Current and (2) the eutrophic, diatomaceous, higher salinity surface waters (chlorophyll-a > 2 mg m−3; S > 33.8) of Monterey Bay and adjacent continental shelf areas. High-resolution and collocated spectrophotometric, fluorometric and CTD data obtained from a towed platform indicated low-salinity subarctic-origin surface waters intruded into Monterey Bay on 4 June. The dark in vivo fluorometry (IVF) phytoplankton response normalized to particle absorption at 676 nm (the apparent fluorescence efficiency, AFE) was nearly fourfold larger in this water mass type compared to higher salinity surface waters more typical of Monterey Bay. The collocated fluorescence and optical data were then used to estimate in situ irradiance values and determine apparent light saturation intensities (I′k) based on the remarkably consistent AFE water column inflection points. I′kvalues retrieved from the low-salinity surface waters were approximately half those obtained over the continental shelf. An analysis of concomitant HPLC data, in addition to historical data for the region, suggest these observed fluorescence trends may be indicative of taxon-specific variation in photophysiology. Specifically, the subarctic water mass-associated pelagic nanoflagellate group likely possesses a fundamentally different photosynthetic architecture than large diatoms prototypical of coastal upwelling regimes.