Pelagic metabolism (community respiration [CR] and net community production [NCP] . Peaks in area-specific NCP were associated with floods, intrusions of nutrient-rich sub-thermocline Coral Sea water, and localized phytoplankton blooms but otherwise showed few seasonal or spatial trends. Overall, CR in GBR lagoon waters was comparable to rates in oligotrophic oceanic waters, but NCP was more typical of shelf systems.The Great Barrier Reef (GBR) is an iconic marine ecosystem 2300 km in length and up to 330 km in width, extending over 15u of latitude (9-24uS). All reefs south of Cape York (10u429S) are contained within the Great Barrier Reef Marine Park (GBRMP), which includes approximately 3700 individual coral reefs (Hopley et al. 2007). Most reefs are located some distance from shore, and the body of water separating the reef matrix from the mainland is locally referred to as the GBR ''lagoon.'' Approximately 90% of the shelf area within the GBRMP (238,700 km 2 ) is comprised of this lagoonal habitat. The GBRMP provides a global reference point for coral reef ecosystems facing threats from the combined effects of terrestrial runoff, overfishing, plagues of pest species such as Crown of Thorns (Acanthaster planci) starfish, and climate change (e.g., coral bleaching). However, inter-reefal and pelagic ecosystems of the GBRMP have received little scientific attention compared to the coral reefs themselves and pelagic process studies have largely focused on the central GBR (16-19uS; Furnas et al. 2005).The GBR lagoon is bordered on the west by low-energy, mangrove-dominated ecosystems with turbid and chlorophyll-rich waters, and to the east it adjoins the matrix of mid-and outer-lagoon reefs perfused by clear oligotrophic waters originating from the Coral Sea. Overall, 73% of the volume of water within the GBRMP to the 150 m isobath is contained in depths of 40 m or less, and in most cases light can penetrate throughout the water column. In the central GBR coastal water moves north via wind-forced currents, but in the mid-and outer-lagoon movement is southward as a result of forcing by the East Australian Current. Southeast trade winds force surface waters onshore, suppressing upwelling on the outer margin of the GBR, but during the northwest monsoon these winds relax and episodic upwelling can occur. Patterns of water circulation in the GBR lagoon are complex and remain poorly understood. On the basis of radium isotope distribution, Hancock et al. (2006) estimated that waters within 20 km of the coast were flushed on timescales of 18-45 d. The numerical models of Luick et al. (2007) predicted flushing times for the GBR lagoon between 1 month and 1 yr, but the drifter studies of Choukroun et al. (2010) suggested this may be less than a month. More than 60% of regional rainfall occurs between the period January and March and is discharged to the coastal waters of the GBR lagoon by river flow. The largest river is the Burdekin River, which has a mean annual flow of 9.7 3 10 9 m 3 , followed by the Normanby ...