The ocean has many underwater light niches, but the selection pressure for chromatic acclimaters (generalists) compared to blue or green-specialists is not well understood. Here, we tested the hypothesis that changes in ocean spectra brought about by mixing on the order of days preferentially selects for generalists within a Synechococcus population. We investigated ocean conditions that led to high proportions of Synechococcus generalists versus specialists in a model ocean column, and compared simulations with in situ metagenomic and physical oceanographic data from major Bio-GO-SHIP cruises, supplemented with GEOTRACES and TARA Oceans, as well as the GOOS Argo Program and sea surface height from AVISO. We found that greater mixed layer depths selected for generalists in simulated Synechococcus populations, but explained only 14% of the partitioning between strategies in situ. Rather, variability due to upwelling and ocean fronts had larger effects, explaining ~40% of the partitioning between Synechococcus generalists and specialists in the ocean. Physical oceanographic drivers therefore offer a significant selection pressure on marine Synechococcus light-harvesting strategies. Our results motivate further study of the in situ light environments of upwelling zones and ocean fronts, which are currently understudied as potential light-driven niche habitats.