A mesocosm experiment was used to investigate the fractionation of silicon (Si)isotopes in subtropical surface waters east of New Zealand. Surface waters in this region were characterised by relatively low concentrations of silicic acid (Si(OH) 4 )(~2 μmol L −1 )and higher nitrate (~5 μmol L −1 )and dissolved iron (Fe)concentrations (~0.4 nmol L −1 )prior to development of the annual springtime phytoplankton bloom. To simulate initiation of the bloom, a large (~700 L)mesocosm experiment was undertaken whereby surface seawater containing the natural plankton community was incubated for a 168-h period. During the mesocosm experiment the concentrations of Si(OH) 4 , nitrate, phosphate and dissolved iron all decreased while the concentration of biogenic silica (BSi)increased 12-fold. Coupled with the increase in BSi was a change in the Si-isotope composition of BSi (δ 30 Si BSi )which increased from 1.49‰ to 2.64‰ after 168 h. Complementary observations to those made for the mesocosm experiment were made for corresponding surface waters. For these waters, we observed a small decline in the concentrations of nitrate, phosphate and dissolved Fe, but little change in the concentrations of Si(OH) 4 and BSi. In contrast to the mesocosm experiment, surface water δ 30 Si BSi values became lighter during bloom initiation, suggestive of Si(OH) 4 being replenished into surface waters. These differences in the drawdown and utilisation of nutrients and dissolved Fe between the mesocosm and surface waters during bloom initiation likely result from favourable Fe and light supply conditions within the mesocosm. In contrast, water column stability (i.e. vertical mixing), and the supply of dissolved Fe are likely to influence bloom initiation and its longevity. The fractionation of Si-isotopes in the mesocosm experiment followed closed-system Rayleigh fractionation kinetics, and an enrichment factor (ε)of −1.13‰ was calculated for the exponential phase of growth for the diatom community, which was marked by the presence of the diatoms Asterionelopsis glacilis and Mellosira moniliformis. The isotope enrichment factor agreed well with previous observations of Si isotope fraction in diatoms from field communities, and appeared to be independent of variations in the ambient Si(OH) 4 concentration, and phytoplankton species composition.