In this paper, a system of flow injection (FI) capillary microextraction (CME) on line coupled with inductively plasma mass spectrometry (ICP-MS) was proposed for simultaneous separation and speciation of inorganic As(III)/As(V) and Cr(III)/Cr(VI) in natural waters. Ordered mesoporous Al2O3 coating was prepared by sol-gel technology and used as CME coating material. Various experimental parameters affecting the capillary microextraction of inorganic arsenic and chromium species have been investigated and optimized. Under the optimized conditions, the limits of detection were 0.7 and 18 ng L(-1) for As(V) and Cr(VI), 3.4 and 74 ng L(-1) for As(III) and Cr(III), respectively, with an enrichment factor of 5 and a sampling frequency of 8h(-1). The relative standard deviations (R.S.D.) were 3.1, 4.0, 2.8 and 3.9% (C=1 ng mL(-1), n=7) for As(V), As(III), Cr(VI) and Cr(III), respectively. The proposed method was successfully applied for the analysis of inorganic arsenic and chromium species in mineral water, tap water and lake water with the recovery of 94-105%. In order to verify the accuracy of the method, two certified reference of GSBZ50027-94 and GSBZ50004-88 water samples were analyzed and the results obtained were in good agreement with the certified values. The ordered mesoporous Al2O3 coated capillary showed an excellent solvent and thermal stability and could be re-used for more than 30 times without decreasing extraction efficiency.