Light-dependent photosynthetic (P-I) responses of size-fractionated (>2 μm, 2 μm fraction. PBm values calculated for near-surface picoplankton (¯ = 6.30) and larger phytoplankton (¯ = 2.87) were five times maximum values in deep-living populations (¯ = 1.24 and 0.57, respectively). Near-surface picoplankton photosynthesized at near-maximal rates over a broad range of irradiances between 400 and 1300 μE m−2s−1, but were photoinhibited at >2200 μE m−2s−1 m−2s−1. Deep-living assemblages of picoplankton and larger phytoplankters became photoinhibited at irradiance levels between 200 and 400 μE m−2s−1. Diurnal time series of photosynthesis measurements made with all size classes of phytoplankton from shallow Great Barrier Reef lagoons had broad midday photosynthesis...

Water Quality Improvement Plans (WQIPs) are being developed for individual river basins on the Great Barrier Reef (GBR) catchment associated with the GBR Water Quality Protection Plan. Within each WQIP, marine ecosystem targets are linked to end-of-river pollutant (suspended sediments, nutrients and pesticides) load targets and to farm level management practice targets. The targets are linked through quantitative models; e.g. one model connects GBR chlorophyll concentrations (marine target) to end-of-river nitrate loads, a second connects the end-of-river nitrate loads to fertiliser management targets in the catchment, whereas a third model links fertiliser application to nitrate loss at the farm scale. The difficulties of applying these linked models to derive credible and practical management targets are great, given the high degree of uncertainty in each model. Our understanding of the generation of suspended sediments, nutrients and pesticides in catchments and the relationship to on-farm management, the transport of these materials to the ocean, their transport in coastal waters and their effects on marine ecosystems is incomplete. The challenge is to produce estimates from the models, with known levels of uncertainty, but robust enough for management purposes. Case studies from the Tully–Murray basin and the Burdekin basin in north Queensland are discussed.

Our view of how water quality effects ecosystems of the Great Barrier Reef (GBR) is largely framed by observed or expected responses of large benthic organisms (corals, algae, seagrasses) to enhanced levels of dissolved nutrients, sediments and other pollutants in reef waters. In the case of nutrients, however, benthic organisms and communities are largely responding to materials which have cycled through and been transformed by pelagic communities dominated by micro-algae (phytoplankton), protozoa, flagellates and bacteria. Because GBR waters are characterised by high ambient light intensities and water temperatures, inputs of nutrients from both internal and external sources are rapidly taken up and converted to organic matter in inter-reefal waters. Phytoplankton growth, pelagic grazing and remineralisation rates are very rapid. Dominant phytoplankton species in GBR waters have in situ growth rates which range from approximately 1 to several doublings per day. To a first approximation, phytoplankton communities and their constituent nutrient content turn over on a daily basis. Relative abundances of dissolved nutrient species strongly indicate N limitation of new biomass formation. Direct ((15)N) and indirect ((14)C) estimates of N demand by phytoplankton indicate dissolved inorganic N pools have turnover times on the order of hours to days. Turnover times for inorganic phosphorus in the water column range from hours to weeks. Because of the rapid assimilation of nutrients by plankton communities, biological responses in benthic communities to changed water quality are more likely driven (at several ecological levels) by organic matter derived from pelagic primary production than by dissolved nutrient stocks alone.

This publication does not have an abstract. The first paragraph of the Introduction is displayed as the abstract. Predicting the effects of contaminant inputs on coastal marine ecosystems has become increasingly important as discharges have increased due to landuse change on watersheds. Coastal pollution from land-based sources and in particular eutrophication are now seen as the principal human threat to coastal seas at a global scale (Correlli, 1998; Carpenter et ai, 1998; Nixon, 1995; Cloem, 2001). To successfully assess the threat to coastal ecosystems from land-based sources of pollution catchment budgets, which determine the relative magnitude of the various sources of contaminants, are necessary. This sort of budgeting has now been carried out in great detail in Europe, North America and the Atlantic Ocean (Howarth et al, 1996; Nixon et al, 1996; De Wit, 2000; Alexander et al, 2002). A similar need is evident for the Great Barrier Reef World heritage Area and its catchment. Such a risk based approach is needed to prioritise catchment management initiatives and compare risk factors within catchments to prioritise works.

This publication does not have an abstract. The first paragraph of the Introduction is displayed as the abstract. Internationally, coral reef systems are under threat from human activity. The International Coral Reef Initiative (Wilkinson, 1999) reported that the condition of over 50% of the world's coral reefs is declining. While the magnitude of threats varies between countries, there are common concerns: over-fishing, uncontrolled development, pollution and global climate change (Wilkinson, 1999). The Great Barrier Reef World Heritage Area (GBRWHA) contains the largest system of coral reefs in the world. This diverse area is more than just coral reefs, it also includes extensive seagrass beds, mangrove forests, sandbanks, sponge and soft coral gardens, and soft bottom habitat and island communities. Of the 2,900 individual reefs, 989 are fringing and/or inshore reefs.

Phytoplankton biomass and primary production rates within semi-enclosed reef lagoons of the central Great Barrier Reef were compared with adjacent shelf waters. Chlorophyll concentrations and surface primary production rates were usually higher in lagoons although seasonal differences were only significant during the summer. Nitrate concentrations were higher in lagoons than in shelf waters year-round. Nano- (<20 μm size fraction) or pico-phytoplankton (<2 μm size fraction) dominated phytoplankton biomass and production within reef lagoons throughout the year. Net phytoplankton (>10–20 μm size fraction), however, were relatively more important in both reef lagoons and open shelf waters during the summer. Biomass-specific production within lagoons (range 41–90 mg C mg chl−1 day−1) was high, regardless of season. Lagoonal phytoplankton production (range 0.2–1.6 g C m−2 day−1) was directly correlated with standing crop and inversely related to lagoon flushing rates. Phytoplankton blooms develop within GBR reef lagoons during intermittent calm periods when water residence times exceed phytoplankton generation times.