Abstract During high- and low-flood periods, surface and bottom water samples were collected along the Nile River estuary for the voltammetric determination of dissolved iodine species. Iodine occurs in the estuary as iodate, iodide and organic iodine. Total iodine increases with salinity, showing a source feature in surface and bottom waters during high-flow indicating iodine input. During low-flow, total iodine showed both addition and removal throughout the course of mixing. Maximum input was associated with turbidity and chlorophyll maxima originating from the agricultural anthropogenic input from Lake Burullus. At the bottom, total iodine enrichment in water matches sulphide production in the anoxic zone. The annual total dissolved iodine flux from the Nile to the S.E. Mediterranean is about 100×10 6 g yr −1 during 1993. Iodate was not measured below salinity 19, nor in the anoxic waters. It is derived mainly from marine waters that contribute between 38–65% and 44–90% of total dissolved iodine during high- and low-flow periods, respectively. Iodate in the surface layer behaves almost conservatively. Iodate behavior during the low-flow period showed three end members: seawater, river, lake water (source) and/or anoxic bottom waters (sink). Iodide, of riverine, marine and sedimentary origins, is almost without exception the dominant iodine fraction in the surface and bottom waters of the Nile estuary. At high- and low-flow periods, iodide showed an increase with salinity in the upper estuary followed by a dramatical decrease seawards beyond salinities 17–23 and 16–28 at surface and bottom layers, respectively. During low-flow, iodine invades the estuary from seawater as iodate which is converted at the bottom layer to iodide by sulphide ion present during anoxic conditions. Organic iodine is a river-derived species, appearing at the surface and bottom waters, coexisting with iodate and iodide in the river side and contributing between 9–40% and 23–29% of total iodine. A flux of 6±2.3 μM I − m −2 day −1 is estimated to be released from the bottom oxic sediments, increasing to 13.4 μM I − m −2 day −1 at the anoxic zone, and is sufficient to raise the iodide concentration to near 500 nM in the bottom waters.