The mechanism of deactivation due to water on the Fischer-Tropsch synthesis (FTS) over alumina supported cobalt catalysts has been studied using steady-state isotopic transient kinetic analysis (SSITKA). This method makes it possible to estimate the concentrations of adsorbed reaction intermediates as well as the time constants involved in the rate determining elementary reaction steps. Both Co/Al2O3 and Co/Re/Al2O3 showed similar deactivation when exposed to water vapour before or during CO hydrogenation reaction. The SSITKA results show that this deactivation is due to loss of active sites, whereas the specific site activity of the remaining active sites is unchanged by the water treatment. This can be explained by assuming that part of the cobalt metal surface is oxidized during the water treatment.