A novel method involving the use of a hydrophobic natural deep eutectic solvent (NADES) in the vortex-assisted liquid-liquid microextraction technique based on the solidification of floating NADES for inorganic Se speciation analysis was developed. In this work, Se(IV) species was selectively complexed with ammonium pyrrolidinedithiocarbamate (APDC) and extracted with 50 μL of the NADES thymol:decanoic acid (THY:DA) (1:2) followed by fast phase separation upon freezing. Se(VI) species remaining in the aqueous phase was directly determined by inductively coupled plasma mass spectrometry (ICP-MS) while total inorganic Se concentration was determined by direct analysis of the acidic extract originated from the samples. Therefore, Se(IV) was calculated by subtracting the concentration of Se(VI) from the total inorganic Se concentration. Extraction conditions such as pH, sample volume, and type and volume of NADES were optimized, yielding an extraction efficiency of 99.6% for Se(IV). Limits of detection of 0.31 μg L−1 for Se(IV) and 0.24 μg L−1 for Se(VI), relative standard deviations of 3.5% for Se(IV) and 3.0% for Se(VI) and a linear range of 0.78–1000 μg L−1 were obtained. This work reports the first application of the NADES THY:DA (1:2) for the separation and determination of Se species in complex matrix samples such as almond, hazel nut, peanut, walnut, cashew nut, pecan nut and Brazil nut.