Hydrogen peroxide (H2O2) is present ubiquitously in marine surface waters where it is a reactive intermediate in the cycling of many trace elements. Photochemical processes are considered the dominant natural H2O2 source, yet cannot explain nanomolar H2O2 concentrations below the photic zone. Here, we determined the concentration of H2O2 in full depth profiles across three ocean basins (Mediterranean Sea, South Atlantic and South Pacific Oceans). To determine the accuracy of H2O2 measurements in the deep ocean we also re-assessed the contribution of interfering species to ‘apparent H2O2’, as analysed by the luminol based chemiluminescence technique. Within the vicinity of coastal oxygen minimum zones, accurate measurement of H2O2 was not possible due to interference from Fe(II). Offshore, in deep (〉1000 m) waters H2O2 concentrations ranged from 0.25 ± 0.27 nM (Mediterranean, Balearics-Algeria) to 2.9 ± 2.2 nM (Mediterranean, Corsica-France). Our results indicate that a dark, pelagic H2O2 production mechanism must occur throughout the deep ocean. A bacterial source of H2O2 is the most likely origin and we show that this source is likely sufficient to account for all of the observed H2O2 in the deep ocean.