Magnetic-based microextraction approaches have gained popularity in recent years due to the magnetic properties of the extraction phases allowing to handle them easier and more efficiently. This work describes a magnetic-based analytical method for the determination of the family of nitro musks in environmental water samples. These compounds have been of great concern due to their environmental impacts and potential health effects. The method is based on stir bar sorptive-dispersive microextraction (SBSDME) as extraction approach, prior to thermal desorption coupled to gas chromatography-mass spectrometry analysis (TD-GC-MS). For this purpose, polydopamine-coated cobalt ferrite magnetic nanoparticles (CoFe2O4@PDA) were used as extraction material. The main parameters involved in the extraction procedure (i.e., sorbent amount, extraction time and ionic strength) as well as in the thermal desorption step (i.e., temperature and desorption time) were evaluated in order to obtain the highest sensitivity. Under the selected conditions, the method showed good linearity, limits of detection and quantification in the low ng L−1 range, intra- and inter-day repeatability with RSD <15%, and high enrichment factors (178–640). Finally, the method was applied to four environmental water samples of different origin. Relative recovery values ranging from 91 to 120% highlighted that the matrices under consideration do not affect the extraction process. This work constitutes the first time in which nitro musks compounds were selectively extracted by taking advantage the high potential that magnetic-based microextraction techniques offer, specially SBSDME.