The characteristics of the phytoplankton crop in the central region of the Great Barrier Reef were analyzed through two annual cycles together with basic oceanographic parameters. Chlorophyll a standing crop and primary production were size fractionated into nanoplankton and microplankton components. Community composition was determined using the Utermöhl settling technique and community diversities estimated by the Shannon-Weaver equation. The data and analysis are the most comprehensive in existence for the region, and the first detailed study since the 1928–29 Great Barrier Reef expedition. A marked seasonal cycle was identified, contrary to most assumptions, closely associated with precipitation patterns and nutrients introduced by land drainage. The region would rank as mesotrophic with some eutrophic areas in the inner reaches of the Lagoon. Oscillatoria spp. accounted for a large fraction of the majority of phytoplankton maxima and were inversely related to diatom crop densities even under conditions favoring diatom growth. Microplankton crop species diversities usually decreased during extended Oscillatoria blooms. The reduced diversity persisted after the bloom suggesting that Oscillatoria spp. were the source of extracellular metabolites and/or decomposition products adversely influencing diatom microplankton.