A novel and miniaturized micro-sequential injection bead-injection lab-on-valve (μSI-BI-LOV) fractionation system was developed for on-line microcolumn soil extraction under simulated environmental scenarios and accurate monitoring of the content of easily mobilisable hexavalent chromium in soil environments at the sub-low parts-per-million level. The flow system integrates dynamic leaching of hexavalent chromium using deionized water as recommended by the German Standard DIN 38414-S4 method; on-line pH adjustment of the extract by a 0.01 mol L⁻¹ Tris–HNO₃ buffer solution; isolation of the chromate leached from the matrix constituents onto a Q Sepharose strong anion-exchanger freshly packed into the microconduits of the μSI-assembly; air-segmented elution of the sorbed species by a 40 µL plug of 0.5 mol L⁻¹ NH₄NO₃ (pH 8) eluent; and detection by electrothermal atomic absorption spectrometry (ETAAS). The effect of simulated acidic rain on the accessibility of chromate forms for plant uptake was also investigated. The proposed approach offers several advantages over conventional speciation/fractionation protocols in the batch mode, including immediate separation with concomitant preconcentration of the released chromate, minimization of Cr(VI) to Cr(III) interconversion risks, enhanced accuracy, and non-existence of re-adsorption/re-distribution problems along with a detailed pattern of the kinetics of the leaching process. The reliability of the proposed method was evaluated via spiking of a moderately polluted agricultural soil material (San Joaquin Soil-Baseline Trace Element Concentrations) with water-soluble Cr(VI) salts at different concentration levels. The potential of the μSI-BI-LOV set-up with renewable surfaces for flame-AAS determination of high levels of readily bioavailable chromate in contaminated soils is also addressed.