The nuchal organ, also referred to as the dorsal organ or neck organ, is a dorsal structure located posteriorly to the compound eye, between the bases of the second antennae of embryonic and neonate branchiopod crustaceans such as the ‘water flea’, Daphnia magna. The ultrastructure of the nuchal organ is similar to ion-transporting tissues in other crustaceans, including abundant mitochondria and extensive amplification of apical and basal plasma membranes through microvilli and infoldings, but direct evidence for ion transport is lacking. We have used the Scanning Ion-selective Electrode Technique to measure transport of Na+, K+, H+, Cl−, NH4+ and Ca2+ across the nuchal organ and body surface of embryos and neonates bathed in dechlorinated Hamilton tap water. Influx of Na+ and efflux of H+ and NH4+ were measured across the nuchal organ of both embryos and neonates. We propose that the efflux of K+ and Cl− across the nuchal organ in embryos is related to the expansion of the haemocoel and release of intracellular solutes into the extracellular space during development. K+ is taken up across the nuchal organ later during development, coincident with expansion of the intracellular compartment through development of gills and other organs. Ca2+ influx across the nuchal organ and body surface of neonates but not embryos is presumably related to calcification of the exoskeleton. Increases in the levels of Na+ and Ca2+ in the water within the brood chamber suggests maternal provisioning of ions for uptake by the embryos. Our data thus support roles of the nuchal organ in ionoregulation, pH regulation, and nitrogenous waste excretion.