A powerful analytical method for the determination of the family of the nitro musk compounds at trace level in environmental waters-river, sea, and water from a treatment plant-is presented. The method is based on the use of molecularly imprinted silica (MIS) as sorbent for solid phase extraction (SPE) used for the clean-up and the concentration step of the target analytes previous to their determination by gas chromatography-mass spectrometry. The optimized extraction procedure allowed extraction recoveries between 61% and 87% using the MIS. The comparison with a non-imprinted silica (NIS) sorbent, for which extraction recoveries between 8% and 26% were obtained, showed the high selectivity of the MIS for the nitro musks. Moreover, high enrichment factors, ranging between 580 and 827, were achieved. The imprinted sorbent was compared to a conventional polymeric SPE sorbent for the extraction of the target compounds from environmental waters, showing high selectivity of the MIS and its clean-up potential. For the first time, the five nitro musk compounds were selectively extracted with an imprinted material.