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Abstract Ocean waves transfer sea spray aerosol (SSA) to the atmosphere, and these SSA particles can be enriched in organic matter relative to salts compared to seawater ratios. A fundamental understanding of the factors controlling the transfer of biogenic organic matter from the ocean to the atmosphere remains elusive. Field studies that focus on understanding the connection between organic species in seawater and SSA are complicated by the numerous processes and sources affecting the composition of aerosols in the marine environment. Here, an isolated ocean–atmosphere system enables direct measurements of the sea–air transfer of different classes of biogenic organic matter over the course of two phytoplankton blooms. By measuring excitation–emission matrices of bulk seawater, the sea surface microlayer, and SSA, we investigate time series of the transfer of fluorescent species including chlorophyll-a, protein-like substances, and humic-like substances. Herein, we show the emergence of different molecular classes in SSA at specific times over the course of a phytoplankton bloom, suggesting that SSA chemical composition changes over time in response to changing ocean biological conditions. We compare the temporal behaviors for the transfer of each component, and discuss the factors contributing to differences in transfer between phases.