The abundance, composition and metabolic activity of plankton were assessed in the Tribulation zone of the central Great Barrier Reef (16°–17°S). Wet phytoplankton biomass ranged in shallow reef waters from 30 to 70 mg m−3, and from 60 to 270 mg m−3 in the deep lagoon and in the estuarine areas which are dominated by pico- and nano-algae. Wet bacterioplankton biomass varied from 70 to 290 mg m−3. Wet meroplankton biomass was less than 10 mg m−3. Wet daytime mesozooplankton biomass ranged from 100 to 300 mg m−3 in the deep lagoon. In the estuarine area, it reached 400 to 1300 mg m−3and in the shallow inner lagoon of the Low Isles ring reef it varied from 10 to 30 mg m−3. Zooplankton density increased at night and was 3 to 5 fold greater in the deep lagoon, for about 2 orders of magnitude greater over the reef shallows and up to 3 orders of magnitude greater in mangrove habitats, due to the emergence of demersal components from the benthos. The biomass of zooplankton hidden in the benthic substrates during the day reached 10 to 40 g m−2. Pelagic primary production in the deep lagoon varied between 0.2 and 0.5 g C m−2 d−1. A calculation of the energy balance suggests that the basic energy source for heterotrophic plankton production in the deep lagoon is the organic matter exported from surrounding reef benthic communities and from mangroves. The trophic status of coral reef pelagic ecosystem might range from mesotrophic to eutrophic.