An automatic on-line solid phase extraction (SPE) system employing the flow injection (FI) technique directly coupled to a graphite furnace atomic absorption spectrometer (GFAAS) was established for speciation and determination of dissolved iron in estuarine and coastal waters. Fe(II) was mixed with ferrozine solution in a sample stream to form the Fe(II)–ferrozine complex which was extracted onto a C18 SPE cartridge, eluted with eluent and detected with GFAAS. In a parallel flow channel, Fe(III) was reduced to Fe(II) with ascorbic acid and then detected in the same way as Fe(II). The home-made interface between FI–SPE and GFAAS efficiently realized the sample introduction to the furnace in a semi-automated way. Parameters of the FI–SPE system and graphite furnace program were optimized based on a univariate experimental design and an orthogonal array design. The salinity effect on the method sensitivity was investigated. The proposed method provided a detection limit of 1.38nmolL −1 for Fe(II) and 1.87nmolL −1 for Fe(II+III). With variation of the sample loading volume, a broadened determination range of 2.5–200nmolL −1 iron could be obtained. The proposed method was successfully applied to analyze iron species in samples collected from the Jiulongjiang Estuary, Fujian, China. With the 2-cartridge FI–SPE system developed, on-line simultaneous determination of Fe species with GFAAS was achieved for the first time.