A series of 19 cruises in 19 months in the central zone of the Great Barrier Reef was made in 1980-1 981 to examine the seasonal thermohaline cycles and nutrient distributions. The reefs occupy the outer 60 km of the shelf and the mixing there of Lagoon Water, Coral Sea Surface Water, Shelf-break Water and Subtropical Lower Water is examined using thermohaline data. Current meters and thermistors were moored from mid-1980 to mid-1982 to obtain seasonal drift and subseasonal temperature fluctuations. Subtropical Lower Water upwells through the reef zone to create a year-round thermal contrast between Shelf-break and Lagoon Waters, and vertical density stratification reflects this temperature contrast on the shelf Salinity variations reflect monsoonal rainfall and winter evaporation; rainfall and salinity show an interannual variation. The drifts of bottom water over the outer lagoon and of surface water over the continental slope follow the isobaths poleward. In the reef zone between the lagoon and the shelf break, there is a substantial cross-isobath, onshore flow of bottom water. Surface waters exhibit no significant averaged gradients in phosphate, nitrate, nitrite or oxygen utilization aross the reef zone. Surface chlorophyll concentration is high amongst the reefs. Subsurface chlorophyll levels are similarly high inside the shelf break, and subsurface phosphate, nitrate and oxygen utilization increases markedly, seaward across the reefs, particularly near the shelf break.