The study consisted of laboratory and field components. Under laboratory conditions, the temperature of standardized individual color chart fields submerged in seawater was determined at contrasting levels of flow and irradiance using a calibrated micro-thermistor with a 1 mm measurement tip. The same method was then used to measure the microtemperature environment around 3 corals (2 massive and 1 branching species) that varied in colony pigmentation from light to dark brown. Coral surface warming at high irradiance (noon) and low irradiance (early morning or late afternoon) in outdoor flow chambers: colonies of the hemispherical species Favia matthai at flow speeds of 1, 2, and 5 cm s-1, and colonies of the digitate species Acropora millepora at flow speeds of 2 and 5 cm s-1. Pigmentation was measured as background fluorescence (F0), determined with pulse-amplitude-modulated fluorometry. The ambient water temperature was 29.38C. In the field, the natural distributions of coral darkness were quantified on 4 reefs across the continental shelf of the Great Barrier Reef, spanning from turbid coastal conditions to clear-water offshore. Reefs were: High Island (a turbid inshore reef with high water nutrient concentrations); Fitzroy Island (an inshore reef with greater water clarity and less exposure to terrestrial runoff from river flood plumes than High Island); Hastings Reef (a mid-to outer-shelf reef, 71% relative distance across the continental shelf); Flynn Reef (on the outermost edge of the continental shelf). Tissue darkness was measured in the first 40 scleractinian coral colonies that were encountered along 6 line intercept transects that ran slope parallel at the windward and leeward side at 4, 8, and 12 m depths (a total of 240 colonies on each reef), including all hard coral species. Measurements of the temperature microenvironment around cnidarians with contrasting darkness on inshore reefs were conducted for 4 consecutive days in January 2005, when sea surface temperatures were 28-29°C, and no signs of coral blanching or bleaching were observed.

To assess the effects and interactions of 3 of the factors involved in controlling the temperature microenvironment of coral colony surfaces, namely irradiance, flow, and colony darkness.

True measures of short-wave radiation, absorptivity, and convection were not attempted: photosynthetically active irradiance was measured as a proxy for short-wave radiation; colony darkness (pigmentation) was used as a proxy for absorptivity; and water flow was manipulated to vary heat convection from the colony surfaces. The use of these variables helped relate the experimental results to underwater measurements that are readily available in the field.Mean visibility across the continental shelf was estimated by spatial models as 5 m at High Island, 8 m at Fitzroy Island, 18 m at Hastings Reef, and 25 m at Flynn Reef. Concentrations of suspended solids and chlorophyll decreased across these reefs.Cnidarians measured on the reef: the flat-encrusting stony coral Montipora tuberculosa, 4 other species of stony corals (including hemispherical, foliose and branching growth forms), two species of octocorals, and the zoanthid Palythoa. Additionally, surface warming was determined in the dark, thick, sediment trapping turf algal mats on these reefs. The experimental tanks measured Favia matthai, Acropora millepora ,and Porites.A standardized coral color chart printed on a thin, lightly textured plastic sheet was used - 'Coral Health Chart', University of Queensland, Australia: www.CoralWatch.org - the 6 color fields on the chart increase on a log scale from score 1=near-white, to score 6=dark brown.