This paper describes the use of an ionic liquid ferrofluid for the preconcentration and simultaneous ultra-trace determination of inorganic As and Se species in waters by inductively coupled plasma mass spectrometry. An ultrasound-assisted sol-gel method was used for the synthesis of silica and titania coated and N-(2-aminoethyl)-3-aminopropyltrimethoxysilane functionalized magnetic nanoparticles (SCTCMNPs-AEAPTMS). The structural features of the SCTCMNPs-AEAPTMS were characterized by Fourier transform infrared spectroscopy, scanning electron microscopy with energy dispersive X-ray spectroscopy, X-ray diffraction, and transmission electron microscopy. Experimental conditions, including the sample solution pH, elution time, and eluent concentration, were optimized. After oxidation of As(III) and Se(IV) to As(V) and Se(VI) by using H2O2, the total concentrations of As and Se were determined and those of As(III) and Se(IV) were obtained through subtraction of the concentration of As(V) and Se(VI) from the total concentrations. Under the optimal experimental conditions, the detection limit for As(V) and Se(VI) were 0.3 ng L-1 and 0.2 ng L-1 respectively. The accuracy of this method was verified by analyzing a certified reference material (1568a Rice Flour): the measured As and Se concentrations agreed with the certified values based on a Student’s t-test at the 95% confidence level. The proposed method was also successfully applied to the preconcentration and ultra-trace determination of As and Se species in different water samples.