The aim of this study was to measure nanoflagellate abundance in New Zealand waters, and identify the key factors which both influence, and are influenced by, nanoflagellate abundance. Nanoflagellate populations were sampled in winter and spring 1993 from a series of sites representing different water masses around the South Island of New Zealand. Both numbers and biomass of heterotrophic (HNF) and autotrophic nanoflagellate (ANF) populations were larger in spring by a factor of four. ANF were about three times as abundant as HNF in both seasons. The physiochemical variables, temperature, NH4‐N, and urea combined with bacteria and picophytoplankton numbers explained between 67 and 94% of the variation in nanoflagellate abundance. In addition, there was evidence that variation in abundances between seasons and water masses was influenced by food availability, predation, and changes in species composition represented by large differences in cell biovolume.