Field observations in Thau Lagoon, southern France, indicate that the growth of natural populations of Alexandrium catenella during blooms is limited by nitrogen and exhibits a storage rather than a growth response to an ammonium pulse. Therefore, ammonium uptake and accumulation under transient conditions were investigated in detail in laboratory cultures. Following nitrogen exhaustion from the medium, ammonium pulses of varying magnitudes were induced, and measurements of extra- and intra-cellular ammonium were carried out for 24–72h along with measurements of ammonium incorporation (15N tracer) and inorganic carbon fixation (13C tracer). During vegetative growth, values of intra-cellular ammonium reached 30% (Strain TL01) and 2% (Strain ACT03) of cell nitrogen. When ammonium was available in the culture medium, ammonium uptake estimated by the 15N tracer technique accounted for only 65% of the decrease in external ammonium. This discrepancy is probably due to organic nitrogen excretion. Once external ammonium was exhausted, the observed isotopic dilution of both 13C and 15N cell content indicated uptake of a compound containing both unlabelled carbon and nitrogen atoms.