In a tank experiment under controlled conditions, the so-called sea spray aerosol chamber, the amino acid and sodium concentrations in the seawater were investigated in 3 cycles (experimental approaches, named as Cycle C1, C2 and C3 within the data set). The seawater samples are ambient North Sea water samples sampled on three different days sampled in April 2017 in the Wadden Sea region of the south-eastern North Sea. The seawater samples were first desalted and concentrated, and for the aerosol samples, the aqueous extract was also concentrated. The concentrated samples were divided into aliquots for analysis of free amino acids and hydrolyzed amino acids (hydrolysis by HCl, 110 ºC for 20 h with addition of ascorbic acid). The processed samples were filtered, derivatized using the AccQ-Tag™ precolumn derivatization method (Waters, Eschborn, Germany), and measured by ultrahigh performance liquid chromatography with electrospray ionization and Orbitrap mass spectrometry (UHPLC/ESI Orbitrap-MS). Exact details of the method used can be found under Triesch et al., 2021a (doi:10.5194/acp-21-163-2021) and Triesch et al. 2021b (doi:10.1021/acsearthspacechem.1c00080). From these, nascent sea spray aerosol particles were generated in the sea spray aerosol chamber using a plunging jet system. The data set reflects the free and combined amino acids and sodium levels in the seawater. Using this data set, conclusions were made about a selective transfer of amino acids from the ocean to the atmosphere under controlled conditions on molecular level. This information could be relevant in the future when parameterizing the organic matter content based on organic compounds and compound classes on marine aerosol particles.