A novel method for the direct determination of mercury species at the ng l−1 level in natural waters is described. Methyl-, ethyl- and inorganic mercury are preconcentrated on a sulphhydryl cotton microcolumn incorporated in a flow injection system. Retained mercury species are then eluted with hydrochloric acid solution (3 mol/l) and subjected to phenylation before determination by gas chromatography-microwave induced plasma-atomic emission spectrometry. Limits of detection for mercury species are 10 ng l−1 for methyl- and ethyl-mercury and 16 ng l−1 for inorganic mercury based on processing 200 ml of sample. Application of the methodology to waters of the Manchester Ship Canal revealed elevated levels of methylmercury and inorganic mercury.