Spatial and temporal scales of variability in phyto- and bacterioplankton abundance were investigated in a deep atoll lagoon (Ahe, French Polynesia), Ahe Lagoon showed a classical phytoplankton composition, but its picophytoplankton (Prochlorococcus, Synechococcus and picoeukaryotes) concentrations are higher than the mean for Polynesian atoll lagoons. Phyto- and bacterioplankton descriptors were highly variable, with mean CVs of >20% in most cases: day night, day-to-day, vertical, lagoonal and seasonal. Phytoplankton biomass, which was estimated by in vivo fluorescence, was higher in the deep layer than in the upper layer. This pattern was detected on a day night scale, showing transitory vertical gradients, and through long-term events that were recorded during day-to-day measurements, especially during low wind conditions. The main factors potentially driving this vertical structure of the phytoplankton appeared to be photoinhibition in upper layers and a bottom effect providing more favourable nutrient conditions in deeper layers. Day-to-day fluctuation was the major source of temporal variation and appeared to be highly driven by vertical patterns and mixing events showing phytoplankton supply from deep layers. At the lagoon scale, the picophytoplankton exhibited a patchy structure that is closely linked to the geomorphology of the rim, lagoon depth and proximity of the pass. Stations close to the pass were characterized by consistently lower Synechococcus and picoeukaryote concentrations. Lastly, warm periods showed higher Synechococcus, nanophytoplankton and bacterial concentrations. Prochlorococcus and picoeukaryotes showed no seasonal trend, but had an annual variability that could be related to variations in exchanges between the lagoon and the ocean.