The widespread diatom Pseudo-nitzschia can produce domoic acid (DA). DA is a compound with well described neurotoxic effects on vertebrates including humans known as amnesic shellfish poisoning (ASP) syndrome. It has also been suggested to serve as an organic ligand that binds to iron and copper. By binding these trace elements, DA may increase their solubility and bioavailability. In order to serve this function, DA has to be excreted and reabsorbed by the cells. Only few records of dissolved domoic acid (dDA) concentrations in the ocean exist. To accomplish quantification by ultra performance liquid chromatography (UPLC), samples have to be pre-concentrated and desalted using solid-phase extraction, a procedure commonly applied for dissolved organic matter. Our major goals were to quantify dDA in a basin-wide assessment in the East Atlantic Ocean, to determine extraction efficiencies for complexed and uncomplexed dDA, and to assess whether domoic acid is represented by its molecular formula in direct-infusion high resolution mass spectrometry. Our results showed that dDA was extracted almost quantitatively and occurred ubiquitously in the ocean surface but also in deeper (and older) water, indicating surprisingly high stability in seawater. The maximum concentration measured was 173 pmol L−1 and the average molar dDA carbon yield was 7.7 ppm. Both carbon yield and dDA concentration decreased with increasing water depth. Providing quantification of dDA in the water column, we seek to improve our understanding of toxic bloom dynamics and the mechanistic understanding of DA production.