A study was carried out to investigate the concentrations of Hg(II) in different categories of water samples at ng L^-1 levels. The capabilities of oxidised carbon nanotubes (ox-CNTs) were studied to assess if this substrate serves as an efficient material for Hg(II) preconcentration using an on-line flow injection cold vapour-atomic absorption spectrometry (FI-CV-AAS) system. Carbon nanotubes are characterized by a marked tendency to aggregate, which negatively affects the retention of Hg whenever integrated in flow systems as a packed column. For this reason, the preconcentration was carried out in a microcolumn filled with a mixture of ox-CNTs and a low molecular weight polyethylene. The preparation of the microcolumn was studied in detail. Concerning column design, the best performance was achieved when packing the substrate in a microcolumn of 2.25 mm (i.d.) × 20 mm length. The effect of chemical and physical parameters including the pH of the solutions, the eluent type and the concentration was systematically examined. Mercury was retained at pH 5.0 and 15% (v/v) HCl was the best alternative for Hg(II) elution. Under optimal conditions, the adsorption capacity of the substrate was found to be 3.2 mg g^-1 reaching a preconcentration factor (PF) of 150. The high adsorption capacity of this substrate allowed reaching a detection limit (3σ) of 1.9 ng L^-1, when using a sorbent column containing only 1.0 mg of ox-CNTs. The limit of quantification (10σ) resulted to be 6.3 ng L^-1. Precision, expressed as relative standard deviation (RSD), turned out to be 1.6% at the 0.1 µg L^-1 level (n = 8). The system was evaluated for quantitative determination of Hg in river water, sea water and effluents.