Flow injection with chemiluminescence detection (FI-CL) was used to determine cobalt and iron in estuarine and coastal waters. Cobalt(II) was determined by means of a pyrogallol–hydrogen peroxide–sodium hydroxide reaction in the presence of methanol and the surfactant cetyltrimethylammonium bromide (CTAB). With pyrogallol, the sensitivity was enhanced compared with the traditional reagent, gallic acid. The practical limit of detection in sea-water was 5 pM (3s) and there was good agreement with certified values for the sea-water CRMs NASS-5 (0.16 ± 0.01 nM), CASS-3 (0.60 ± 0.09 nM) and SLEW-2 (0.93 ± 0.13 nM). Results for an Irish Sea sample gave good agreement with data obtained using cathodic stripping voltammetry. Iron(II + III) was determined using a luminol reaction with dissolved oxygen as the oxidant. The practical limit of detection was 40 pM (3s) and results from shipboard analysis of the CRM NASS-4 (1.95 ± 0.14 nM) were in good agreement with the certified value (1.88 ± 0.29 nM). Field evaluation of the instrumentation and analytical methods was achieved through a series of local surveys in the Tamar Estuary (UK), from which environmental data are presented.