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Inorganic mercury and methylmercury are determined in natural waters by injecting the filtered samples onto a low cost commercial flow injection system in which an anion exchange microcolumn is inserted after the injection loop (FIA-IE). If hydrochloric acid is used as the carrier solution, the HgCl4(2-) species (inorganic mercury) will be retained by the anion exchanger while the CH3HgCI species (methylmercury) will flow through the resin with negligible retention. Four anion exchangers and seven elution agents were checked, in a batch mode, to search for the best conditions for optimal separation and elution of both species. Dowex M-41 and L-cysteine were finally selected. Mercury detection was performed by cold vapour-electrothermal atomic adsorption spectrometry (HG-ETAAS). Both systems were coupled to perform the continuous on-line separation/detection of both inorganic mercury and methylmercury species. Separation and detection conditions were optimized by two chemometric approaches: full factorial design and central composite design. A limit of detection of 0.4 microg L(-1) was obtained for both mercury species (RSD < 3.0% for 20 microg L(-1) inorganic and methylmercury solutions). The method was applied to mercury speciation in natural waters of the Nerbioi-lbaizabal estuary (Bilbao, North of Spain) and recoveries of more than 95% were obtained.