It has been reported that antidepressant, anxiolytic and antihypertensive drugs alter the behavior and reproduction of the microcrustacean Daphnia magna at very low concentrations. However, there is little evidence for how these drugs act on their neurotransmitter targets. A method based on hydrophilic interaction liquid chromatography coupled with tandem mass spectrometry has been developed and applied for the first time using D. magna extracts and validated by studying the changes in the levels of a suite of neurotransmitters caused by five different neuroactive pharmaceuticals (fluoxetine, venlafaxine, carbamazepine, propranolol, and diazepam) dosed at 100 ng/L. Sample extraction and chromatographic and detection conditions were optimized for accurate detection of the selected neurotransmitters in whole D. magna organisms. The method allowed the simultaneous quantification of eight neurotransmitters belonging to six neuroendocrine systems: the dopaminergic, adrenergic, GABAergic, serotoninergic, histaminergic, and cholinergic systems. Neurotransmitters were eluted with a ZIC-HILIC column and quantified by tandem mass spectrometry in positive electrospray ionization mode performed in multiple reaction monitoring mode. All method validation assays (i.e., quality controls for linearity, sensitivity, accuracy, precision, stability, recovery, matrix effect, and carryover) were compliant with the standard requirements for similar analysis. Exposure to fluoxetine enhanced serotonin concentrations, whereas exposure to diazepam decreased the levels of dopamine, and exposure to propranolol increased the levels of norepinephrine. Exposure to both propranolol and diazepam decreased the levels of histamine. The results show the usefulness of this approach for environmental neurotoxicity studies. Graphical abstract.