A flow-injection system is developed for Cu, Mn and Zn partitioning in seawater by flame atomic absorption spectrometry. The first approach is where the trace metal species are fractionated in situ, but analysis is performed by using a flow injection manifold in the laboratory. This operational mode is used for the determination of the dissolved labile metallic fraction and is based on the elution of this fraction from a minicolumn packed with a chelating resin containing iminodiacetic acid groups (Serdolit Chelite Che) loaded in situ with the sample. The second is used for the determination of total dissolved concentrations of trace metals. This last mode is based on the retention/preconcentration of total dissolved metals on the chelating resin after on-line sonolysis of seawater samples acidified with diluted nitric acid to breakdown the metal–organic matter complexes. The figures of merit for Cu, Mn and Zn determinations in both fractions are given and the obtained values are discussed. The fractionation scheme is applied to the analysis of coastal seawater samples collected in Galicia (Northwest, Spain). The results of fractionation showed that Mn and Zn are mainly in the labile fraction, while Cu was mainly present in the organic fraction.