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In a three-week pelagic estuarine enclosure experiment, no effect concentrations (NEC) for tri-butyl-tin (TBT) were found in phytoplankton in the lower pico molar (pM) range as indicated by increased TBT tolerance, changes in taxonomic composition, decreased primary production and in the chlorophyll a (chl. a) concentration. Decreased primary production and chl.a concentrations were found only three days after addition of TBT. On the other hand, taxonomic changes and increased tolerance were found throughout the experiment, indicating a recovery of the ecosystem caused by adaptation of the phytoplankton in terms of structural changes. Induction of TBT tolerance is assumed to be evident of a direct toxic effect of TBT on the phytoplankton and the observed effects are thus not just attributable to indirect effect caused by direct effects on e.g. zooplankton. TBT concentrations in the lower pM range in coastal waters, such as open bays and estuaries, have been reported, indicating that natural phytoplankton could be affected by TBT in such areas.