Corresponding author: M. C. MacKellar, Climate Research Group, School of Geography, Planning and Environmental Management, The University of Queensland, Brisbane, Qld 4072, Australia. (email@example.com)
 Measurements of the surface energy balance, the structure and evolution of the convective atmospheric reef layer (CARL), and local meteorology and hydrodynamics were made during June 2009 and February 2010 at Heron Reef, Australia, to establish the relative partitioning of heating within the water and atmosphere. Horizontal advection was shown to moderate temperature in the CARL and the water, having a cooling influence on the atmosphere, and providing an additional source or sink of energy to the water overlying the reef, depending on tide. The key driver of atmospheric heating was surface sensible heat flux, while heating of the reef water was primarily due to solar radiation, and thermal conduction and convection from the reef substrate. Heating and cooling processes were more defined during winter due to higher sensible and latent heat fluxes and strong diurnal evolution of the CARL. Sudden increases in water temperature were associated with inundation of warmer oceanic water during the flood tide, particularly in winter due to enhanced nocturnal cooling of water overlying the reef. Similarly, cooling of the water over the reef occurred during the ebb tide as heat was transported off the reef to the surrounding ocean. While these results are the first to shed light on the heat budget of a coral reef and overlying CARL, longer-term, systematic measurements of reef thermal budgets are needed under a range of meteorological and hydrodynamic conditions, and across various reef types to elucidate the influence on larger-scale oceanic and atmospheric processes. This is essential for understanding the role of coral reefs in tropical and sub-tropical meteorology; the physical processes that take place during coral bleaching events, and coral and algal community dynamics on coral reefs.
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net horizontal advection and diffusion of heat within the water column.
addition or loss of sensible heat due to rainfall.
heat transfer via conduction and radiation by the substrate and benthic cover.
energy transferred into the water column, benthos, and substrate.
heat flux through the water surface.
heat flux into water from substrate and benthic cover.
heat gain due to radiative processes in the water.
net radiation at the sea floor.
advection of heat due to large scale weather systems.
horizontal advection of heat due to local air flow.
heating due to radiative processes in the CARL.
latent heat flux due to condensation in clouds.
net radiation at the top of the CARL.
 The heat budget of the water and lower atmosphere overlying coral reefs is controlled by complex interactions between hydrodynamics (water depth, currents, and temperature), the surface energy balance (air-reef radiation transfers, heat and moisture fluxes, biogenic aerosols), local atmospheric thermodynamics, and the prevailing synoptic meteorology. Understanding of the physical mechanisms that underpin the thermal environment of coral reefs, which have been estimated to cover 255,000 km2 [Spalding and Grenfell, 1997], may facilitate more accurate prediction of the weather and climate of coral reefs and surrounding environments, including cloud and rainfall patterns, development of local winds, and the genesis and intensification of tropical cyclones. Understanding of the interrelationships between surface radiative forcings, heat and moisture fluxes, boundary layer structure, and surface properties is “fundamental for the realistic incorporation of the boundary layer into large-scale models… and to enable direct prediction of fundamental boundary layer parameters” [Cattle and Weston, 1975, pp 1]. Furthermore, observational studies as we present here are necessary for evaluating numerical model simulations of large-scale circulation and ocean-atmosphere coupling in the tropics [Johnson et al., 2001]. The study of the heat budget of coral reefs is essential also for accurate prediction of the impacts of climate change on coral reefs, including coral bleaching. Elevated sea surface temperatures (SST) and/or rising sea levels have the potential to significantly alter the thermal environment of coral reefs with a range of adverse effects for corals and their inhabitants, which live within a narrow range of environmental tolerances [McCabe et al., 2010]. Therefore, direct measurements of reef-atmosphere interactions are important for predicting the likely consequences of anthropogenic climate change on coral reef environments. Research may also elucidate spatial “patchiness” in coral bleaching severity due to variation in environmental stressors (e.g., thermal and radiation extremes), and/or improve understanding of local diversity in population and community dynamics of reef organisms [Lenihan et al., 2008].
 Despite the linkages between heat exchange processes in the water and the overlying atmosphere, the few studies that have described coral reef thermal budgets have largely ignored the latter, focusing solely on heat partitioning in the water. Thermal budgets for water bodies have been conducted over the open ocean, for example, south of Japan for the Ocean Mixed Layer Experiment (OMLET) [Kurasawa et al., 1983; Tsukamoto et al., 1995], in mangrove environments [Nihei et al., 2002b], and lakes [den Hartog et al., 1994; Momii and Ito, 2008; Rouse et al., 2005]. Over coral reefs, such studies have mostly lacked direct measurements, relying on measurements of basic meteorological parameters only, sometimes at upwind terrestrial sites which have then been used to indirectly calculate air-sea heat and moisture fluxes using bulk aerodynamic formulas [Davis et al., 2011; Kjerfve, 1978; McCabe et al., 2010; Monismith et al., 2006; Nihei et al., 2002a]. Nadaoka et al.  used a simplified heat budget model to investigate the hydrodynamic and thermal environment of Shiraho Reef, Ishigaki Island, southwest of Japan. At the same location, Nihei et al. [2002a, 2002b] later demonstrated the important contribution to the heat balance made by conductive heat transfers from the sea floor to the overlying water of shallow reefs. As a result, they added a term for heat input by the sea floor (Hsoil) to their model, in addition to estimating the heat gain due to radiative processes in the water (Sabs). Davis et al.  adopted a simple model, similar to Nihei et al. [2002a], for estimating temporal and spatial variability in water temperature over a platform reef in the Red Sea. They assumed that the influence of Hsoil was negligible and used bulk formulas to derive air-sea fluxes using meteorological data from 30 km offshore of Abu Madafi reef in water 700 m deep and from a terrestrial site. Despite their assumptions, the model performed well, predicting water temperature on the outer shelf of three reefs within 0.4°C using basic bathymetry, surface heat flux, and offshore wave parameters only. Key spatial differences in water temperature on each reef were also identified and were largest when the air-sea fluxes were high and horizontal advection was low.
 At Heron Reef on the southern Great Barrier Reef, MacKellar et al. [2012a] highlighted spatial variation in water surface temperature (Tsurf) across the reef with differences of up to 2.8°C and 1.9°C between the reef flat and deep lagoon, and reef flat and shallow lagoon, respectively. They attributed this spatial heterogeneity to different water depths and underlying benthos. McCabe et al.  made temperature measurements over the shallow lagoon and reef flat of Lady Elliot Island, south of Heron Reef, and attempted to model (via a simple analytical approach) lagoon temperature using a well-mixed control volume approach. The model performed well although a shortcoming was its inability to predict sudden changes in temperature associated with warm water influx with the rising tide. They applied a “frontal” modification parameter to their model with improved predictive success.
 Whilst these studies have provided some insight into the heating and cooling rates of the water overlying coral reefs, they do not describe the thermal budget of the overlying convective atmospheric reef layer (CARL), the internal atmospheric boundary layer that develops downwind of the sea-reef interface. In coastal environments, atmospheric heat budget analyses have focused particularly on the influence of the sea breeze circulation across the ocean-land boundary [Kuwagata et al., 1994; McGowan and Sturman, 2005]. Kuwagata et al.  made observations of the thermal effect of the sea breeze on ABL structure and its heat budget over complex terrain in central Japan. Their observations showed that the heating rates were higher near the valley floor due to warming associated with daytime subsidence, compared with the surrounding mountainous areas. In coastal areas, the sea breeze was also found to decrease the overall heating rate. Kuwagata et al.  conducted a similar study focussing on the effect of the sea breeze circulation across the Sendai Plain, Japan. They showed that, despite a horizontal temperature gradient of over 10°C during sea breeze conditions, horizontal advection of warmer air in the counter flow aloft meant that the overall heating rate showed no difference between the coastal and inland sites. A study of the heating and cooling of the ABL was also conducted by McGowan and Sturman  over a coastal plain in Manawatu, New Zealand. Surface heating and upward propagation of heat were observed throughout the day, in addition to entrainment of heat from aloft due to shear-induced turbulence or penetrative convective plumes. They applied the heat budget model by Kuwagata et al.  and found that heating due to QH increased with distance inland and that cloudy periods resulted in a decrease in surface heating, and an addition of heat due to condensation and advection.
 Whilst a small body of research has begun to shed light on the thermal heat budgets for the water over coral reefs, no study has yet presented heat budget estimates for both the marine and atmospheric components, nor described their interrelationships. Accordingly, this study presents the first estimates of a heat budget for a coral reef for both the water overlying the reef and the atmospheric boundary layer. Measurements were made during 11–14 June 2009 and 9–12 February 2010 (henceforth referred to as June 2009 and February 2010). The overarching aim was to provide insight to the physical processes that underpin thermal conditions both above and below the water surface of a coral reef.
2 Site Description
 Heron Reef is located approximately 80 km northeast of Gladstone, on Australia's east coast, in the Capricorn-Bunker Group of reefs in the southern Great Barrier Reef (Figure 1). The reef covers 27 km2 and is considered representative of platform reefs in the region [Jell and Flood, 1978], characterized by distinct hydrodynamic and geomorphic zones, and benthic assemblages [Flood, 1978]. Heron Reef is separated from nearby Wistari Reef by a 25 m deep channel with Sykes and One Tree Reefs located to the east and southeast.
 Rainfall at Heron Island, a small coral cay located on the western margin of Heron Reef, is bimodal with the largest falls during summer, followed by autumn with an annual average total of 1050 mm. During the summer, the Intertropical Convergence Zone moves southward bringing convective rain to the region [Sturman and McGowan, 1999]. The average temperature at 1500 Eastern Standard Time (EST) is highest in January at 28.3°C and lowest in July at 20.1°C [Bureau of Meteorology, 2012]. The prevailing south-east trade winds affect Heron Reef year round with occasional wintertime westerlies and a greater prevalence of warm northerly winds during the summer.
 Tides at Heron Reef are semidiurnal and the average spring and neap tidal ranges are 2.28 and 1.09 m, respectively [Chen and Krol, 1997]. Under a mean wind speed of 5 m s−1, the average wave height and maximum current velocity across the reef flat are 0.5 m and 0.3 m s−1 or <0.6 times the maximum water level [Gourlay and Hacker, 1999]. At low tide, reef top water is isolated by the emergent reef rim, whilst the oceanic wave field influences wave action across the reef flat when the tide rises above the reef rim. The prevailing south-easterly trade winds produce moderate seas which are sometimes enhanced by sea breeze waves. During February and June, significant wave heights at the nearest Wave-rider buoy (approximately 100 km northwest of Heron Reef) are 0.96 and 0.7 m, respectively with the dominant wave direction from the north-east and the east-south-east, respectively (DERM 2004). For the months of February and June, data from an Integrated Marine Observing System (IMOS) sensor float in the deep lagoon of Heron Reef showed an average water temperature (0.6 m below the surface) of 27.3°C and 21.5°C, respectively.
3.1 Energy Balance Measurements
 Measurements of the surface energy balance were made using an eddy covariance (EC) unit mounted on a pontoon over the shallow reef flat [MacKellar et al., 2012a]. The EC unit consisted of a Campbell Scientific CSAT-3 sonic anemometer (Ux < ±4.0 cm s−1, Uy and Uz < ±2.0 cm s−1), a Kipp and Zonen CNR1 net radiometer (spectral range 0.3–50 µm), and a Vaisala HMP45A sensor-recorded ambient Tair (±0.2°C) and relative humidity (±2.5%). The height of all instruments was 2.2 m above the water surface with data collected by a Campbell Scientific CR23X data logger during June 2009 and a CR3000 data logger in February 2010. Measurements were made at 10 Hz with 15 min block averages logged.
 Water depth and near bottom water temperature (Tbottom) were measured with HOBO U20-001-01 water level sensors (accuracy 0.21 cm, ±0.37 °C at 20°C), and HOBO water temperature PROV2 loggers (±0.2°C) provided the Tsurf at a depth of 0.05 m below the surface. During February 2010, an additional Tsurf measurement was made with a Campbell Scientific model 107 temperature probe (<±0.2°C). Instrumentation was factory calibrated before deployment and serviced daily to ensure sensors were level and free from salt scale and algae. Eddy covariance data were corrected for frequency attenuation [MacKellar et al., 2012a; Massman and Lee, 2002] and density effects [Webb et al., 1980]. Two-dimensional coordinate rotation was performed on the data to correct for possible tilt errors [Lee et al., 2004], and anomalous data spikes were removed.
3.2 Boundary Layer Measurements
 Aerological soundings of the lower troposphere (<600 m) were made with a tethersonde during June 2009 and a Kestrel 4500 weather monitor (temperature ±1°C, relative humidity ±3%, air pressure ±1.5 hPa) during February 2010. The instruments logged atmospheric pressure, Tair, relative humidity, and wind speed and direction at 10 s intervals and were tethered to a kite when winds exceeded 5 m s−1, or helium-inflated Helikite at lower wind speeds [see MacKellar et al., 2012b]. Flights were conducted from the windward shoreline on the eastern side of Heron Island due to its proximity to the reef to mitigate any possible influence of the island on soundings. These ascents reached a maximum height of approximately 600 m with the kite and 200 m with the Helikite above sea level with a height accuracy of approximately ±10 m. All surface values of the soundings were cross checked with separate reference surface measurements made with a handheld Kestrel 4500 and were subjectively screened for spurious data points.
 Data from the soundings were used to calculate vertical profiles of mixing ratio and virtual potential temperature (θv). Surface measurements of meteorological variables such as Tair, absolute humidity (q), wind speed and direction, and pressure were provided by the HMP45A. A Vaisala CL-31 ceilometer measured cloud base height and cloud thickness up to a maximum height of 7500 m during the field campaign as well as boundary-layer height with a vertical measurement resolution of approximately 10 m.
4 Heat Budget Models
 The heat budget for Heron Reef was analyzed for (1) the CARL, defined here as the internal thermal boundary layer that develops within the marine atmospheric boundary layer above the reef in response to changes in the surface properties across the reef-ocean interface [see MacKellar et al., 2012b for a detailed description of the marine atmospheric boundary layer over Heron Reef], (2) the reef-water-surface-atmosphere interface, (3) the volume of water overlying the reef, and (4) across the reef substrate. The heating rate of a unit volume essentially equates to the summation of the heat fluxes through the boundaries of the system [Saur and Anderson, 1956]. The parameters that contribute to the heating rate of the CARL (QBL) and the water column (Qwater) are illustrated in Figure 2.
4.1 Air-Reef Interface
 The energy balance of the water surface at Heron Reef can be written as
where Q* equates to the net all wave radiation or the sum of incoming and outgoing shortwave radiation (K↓ and K↑) and longwave radiation (L↓ and L↑), QE is the latent heat flux and QH the sensible heat flux. These parameters were all measured directly. The net horizontal advection of heat in the water by currents is denoted by ΔF, while QR is the addition or lossof heat associated with rainfall. The heat transfer via conduction and radiation transfers into or out of the reef substrate is termed Gsoil [McGowan et al., 2010]. During the case study periods presented here, measurements affected by precipitation were removed (QR). The remaining terms (Qwater, ΔF, and Gsoil) were grouped (QSWR) and determined as the residual of equation (1), which is a common approach when direct measurements of these parameters are not practical [Kurasawa et al., 1983; MacKellar and McGowan, 2010; McGowan et al., 2010; Tsukamoto et al., 1995]. Accordingly, the simplified surface energy balance equation was rewritten as
4.2 Heat Budget for the Water Column and Substrate
 The heat budget for a volume of water overlying the shallow lagoon during June 2009 and the reef flat during February 2010 was calculated following Nihei et al. [2002a] every 15 min as
where Qwater is composed of the summation of ΔF, Hsoil, the heat flux through the water surface (QG), and heat gain due to absorption of shortwave radiation by the water (Sabs). At near-shore sites, the contribution of groundwater, which percolates laterally out of the coral cay, may also affect the heat balance of the water. In this study, however, measurements were made at sufficient distance from the cay that it was considered negligible and therefore not considered further. Using the specific heat of water (≈4200 J kg−1 K−1), Qwater was calculated using the measured water depth and water temperatures (average Tsurf and Tbottom) to calculate the energy required to heat the volume of water during each 15 min period. Calculations of QG and Sabs were conducted using equations (4) and (5), respectively, while ΔF was determined as the residual of equation (3).
 In equation (4), QG was determined as the equation residual and only the longwave radiative component was included because shortwave radiation was already accounted for in the term Sabs. Equation (5) was used to calculate Hsoil, where the terms on the right-hand side of the equation represent the net radiation on the sea floor (Q*sub).
 Direct measurements of Gsoil were made with HFT ground heat flux plates (accuracy ±3–5% of reading) buried approximately 10 mm below the surface of the coral sand on the reef, and Hsoil was calculated as the residual of the equation. Given the complexity of doing so, direct measurement was not made with respect to any heat contribution by the benthic coral cover and we have assumed that this parameter is included in Hsoil.
 The albedo on the reef floor (α2) was taken to be 0.25 according to laboratory measurements by Nihei et al. [2002a] on coral sand. The albedo of the water surface (α1) was obtained by subtracting the albedo measured by the CNR1 net radiometer from α2. During the daylight hours when K↓ was positive, the α1 averaged 0.06 (average range 0.05–0.1) from 9–12 February 2010 and 0.08 (average range 0.04–0.15) during the June 2009 field campaign. The extinction coefficient (βh) of shortwave radiation in water was taken from measurements of downwelling irradiance profiles on the southern side of Heron Reef in 5–10 m of water, where the average βh for wavelengths 350–1050 nm was 0.6 m−1. Finally, ΔF was determined as the residual of equation (3) and the expression for Sabs was given by equation (6):
4.3 Convective Atmospheric Reef Layer (CARL)
 The CARL develops over the coral reef surface within the mixed marine atmospheric boundary layer (observed to vary in height from 375 to 1200 m above sea level (asl) at Heron Reef; see MacKellar et al., [2012b]) in response to horizontal differences in the surface energy balance and roughness between the reef and ocean surfaces. The energy balance is mixed into the atmosphere via turbulence as air flows across the ocean-reef boundary, creating the internal CARL. At Heron Reef, this layer was observed to reach a maximum height of approximately 135 m asl [MacKellar et al., 2012b]. This layer is often stably stratified during the early morning and evening, becoming unstable during the day following the onset of surface heating and an increase in QH [MacKellar et al., 2012b]. Following Kuwagata et al.  and McGowan and Sturman , the heat budget for an idealized control volume of the ABL can be calculated according to equation (7) where QBL is the heating rate of a volume of air in the atmosphere:
 In this equation, Qsyn is the advection of heat into the boundary layer associated with large scale weather systems, Qadv represents the energy gain/loss due to horizontal airflow through the volume, Q*BL is the net heat or gain of energy through radiative processes, and Qcon is the latent heat flux due to condensation in clouds within the layer. Cloud was absent from the CARL during our observation days, allowing Qcon to be neglected; Qsyn was assumed to be zero as there was no significant change in the synoptic air mass above the CARL [McGowan and Sturman, 2005], whilst Qadv was calculated as the residual value of equation (7). Equation (8) was then used to calculate Q*BL, which incorporates Q* and the net radiation at the top of the CARL (Q*2):
 In order to derive Q*2, Beer's law was applied using extinction coefficients obtained from reanalysis data using the Weather Research and Forecasting (WRF) Model. The extinction coefficient for the wavelength 550 nm was used as a proxy for net all-wave radiation. Given that the lowest extinction coefficients occur in this wavelength, and that shorter and longer wavelengths are more quickly attenuated in the atmosphere, this may yield the minimum values for Q*BL. The heat budget was calculated for the lowest 60 m asl of the CARL for periods between atmospheric soundings on 14 June 2009 and 12 February 2010 when settled, anticyclonic conditions prevailed. The lowest 60 m asl was chosen as it corresponded with the minimum height of the CARL during the observations presented here.
5.1 Meteorological and Hydrodynamic Overview
 From 11–14 June 2009, the wind direction gradually shifted from the south to the south-east as a high pressure cell moved east off the coast of eastern Australia (Figure 3), resulting in a shift from cool, dry conditions on 11 June 2009 to warmer and more humid maritime conditions (see Table 1). During the summer observation period, the wind direction changed from the south-east on 9 and 10 February, to the north-east and east on 11 and 12 February, respectively. Wind speeds were lower during the summer observation period, whilst the average Tair was 26.9°C, compared to 19.1°C in winter, and average q was 8.5 g m−3 higher than the winter days at 17.9 g m−3.
Table 1. Average Daily (24 h) Meteorological, Hydrodynamic, and Heat Budget Variables for 11–14 June 2009 Over the Shallow Lagoon and 10–12 February 2010 Over the Reef Flat at Heron Reef
q (g m−3)
Wind speed (m s−1)
Wind direction (°)
Tidal range (m)
Q* (W m−2)
QE (W m−2)
QH (W m−2)
QSWR (W m−2)
Qwater (W m−2)
QG (W m−2)
Hsoil (W m−2)
Sabs (W m−2)
ΔF (W m−2)
Gsoil (W m−2)
s (W m−2)
 During June 2009, the tidal range in the shallow lagoon of Heron Reef decreased from 1.7 m on 9 June to 1.4 m on 14 June. The minimum water level was 0.7 m each day (Figure 3). By comparison, during February 2010 at the reef flat, the tidal range was higher due to continued drainage throughout the ebb tide. The highest tidal range occurred on 12 February 2010 when the low tide was <0.2 m at 1600 EST, exposing coral on the reef. During the February 2010 observation period, the afternoon low tide coincided with the daily maximum Tsurf. On 11 and 12 June, maximum Tsurf occurred between 1330 and 1400 EST, prior to cooling of the water during the afternoon ebb tide when QE and QH were the highest. On the subsequent days, Tsurf peaked in the afternoon, before QSWR became negative.
5.2 Coral Reef Surface Energy Budget
 During the February 2010 observation days, maximum Q* coincided with maximum solar azimuth and decreased during cloudy periods (Figure 4a), while the daily average Q* (197.4 W m−2) was 3.7 times larger than during the June 2009 field campaign (53.4 W m−2). The proportion of Q* partitioned into QSWR between 1030 and 1430 EST ranged from 20.5% to 66.1% during 11–14 June 2009, increasing during the summer case study to 71.2–87%. On average for the entire summer period, QE, QH, and QSWR accounted for approximately 74%, 7%, and 16% of available Q*. During winter, however, the turbulent fluxes (QE and QH) exceeded Q* resulting in a net loss of heat from the water, substrate, and benthos (QSWR < 0 W m−2) and cooling of the water overlying the reef. The highest turbulent fluxes occurred during the morning of 11 June 2009 (Figure 4a) when cool, strong southerly winds were present.
5.3 Heat Budget for the Sea Floor and Water Column
 Owing to higher K↓ and shallower waters during February 2010, the heat fluxes at the reef substrate were higher than during June 2009 (Figure 4b). Over 95% of Q*sub was partitioned into Hsoil during the summer study, while a small amount during the daytime was absorbed by the coral sand (Gsoil). Average daily Gsoil was typically negative during June 2009 at the shallow lagoon except on 14 June 2009 when it was positive (albeit low at only 1.6 W m−2). This was due to a higher Gsoil minimum during the morning low tide of 6.4 W m−2 at 700 EST, compared to −42.6 W m−2 at 900 EST on 12 June 2009 when turbulent fluxes were high and the Tsurf and Tbottom decreased sharply (Figure 3a).
 Consistently negative QG values were recorded during both the summer and winter campaigns, indicating cooling of the water column via longwave radiation and the turbulent flux exchange (Figure 4c). During the winter observation days, ΔF was typically a source of heat to the shallow lagoon, particularly during the morning when sharp increases in water temperature were associated with the rising tide. These spikes in ΔF occurred when the water level exceeded 1.2 m, indicating the level at which the tide flooded the shallow lagoon with warmer oceanic water and enhanced mixing by advection. For example, between midnight and 800 EST on 11 June 2009, the high QE and QH resulted in a decrease in Tsurf of 3.7°C on the reef flat where, due to the lower thermal capacity, cooling was more pronounced than over surrounding ocean. At 930 EST when the water level reached 1.4 m, Tsurf and Tbottom increased by 2°C in a 30 min period. This increase in temperature is likely to have been exacerbated by mixing due to the strong winds (over 9 m s−1) that would have enhanced wave action over the shallow lagoon [MacKellar et al., 2012a]. A second, smaller spike in ΔF occurred around midnight during the winter observation days when the higher high tide occurred (>2.1 m; Figure 4c). On the falling tide, ΔF decreased rapidly and stabilized near zero until the next tidal change, presumably due to pooling of reef water in the shallow lagoon. On 11 and 12 June 2009, prior to these ΔF spikes, short, sharp decreases in water temperature (and ΔF) were observed, corresponding with the start of the flood tide. This may have indicated the advection of cooler water from over the shallower reef flat, which lies between the shallow lagoon and ocean. During 9–12 February 2009, ΔF fluctuated with the tide in a similar nature, albeit at a lower magnitude.
5.4 Case study Heat Budgets for the Reef and Lower Troposphere
 On 14 June 2009, a clear diurnal signal of CARL evolution was observed over Heron Reef (Figure 5a) yet the heating and cooling of the water column were less prominent than earlier in the observation period due to lower turbulent fluxes and a smaller range in water level. The influence of Q*BL was minor throughout the day with radiative divergence between the surface and the top of the CARL of <1%. Between 0720 and 1000 EST Tsurf increased by 0.05°C h−1 (Qwater of 92.4 W m−2 h−1), primarily due to Hsoil and Sabs, while ΔF transported −42.6 W m−2 h−1 away from the reef with the falling tide (Figure 6a). In response to the surface heating, the θv profile changed from an inversion to a lapse, signifying unstable conditions (Figure 5a). Accordingly, this change in the profile resulted in cooling within the CARL by an average of −2.2°C, corresponding with a total hourly QBL of −7.2 W m−2 h−1 with an increase in cooling with height. An increase in QH between 1000 and 1415 EST (17.6 W m−2 h−1) resulted in CARL growth (to around 100 m asl shown in Figure 5a), yet QBL remained fairly low (0.5 W m−2 h−1) due to higher Qadv as the surface wind speed increased to 3.9 m s−1. During this period, the water was 1 m deeper, yet Qwater was exacerbated (620.7 W m−2 h−1) due to higher Sabs and Hsoil, with ΔF also contributing 322.9 W m−2 h−1 as warmer oceanic water inundated the reef with the rising tide (Figure 6b). During the afternoon period (1415–1600 EST), QBL was the highest (5.1 W m−2 h−1) and the heating rate increased with height above the reef water surface (Figure 5b), as heat propagated upward, resulting in more mixed profiles of θv and Tair by 1600 EST. During the same period, Qwater had decreased due to lower K↓ and a falling tide which resulted in lower ΔF (52.2 W m−2 h−1) (Figure 6c).
 On 12 February 2010 under settled anticyclonic conditions, the lower level of the marine atmospheric boundary layer was less stratified and the CARL was not as clearly defined as on 14 June 2009 resulting in less temperature variation (Figure 5b). The influence of Q*BL remained small; however, it was greater than on 14 June 2009, contributing up to 1.6 W m−2 h−1 during the afternoon. This was primarily due to higher K↓ and higher q, as well as possibly elevated atmospheric aerosol, such as dimethylsulfide (DMS). There is now good evidence that corals produce atmospheric DMS [Fischer and Jones, 2012] that could take part in marine aerosol formation events over reefs such as Heron Island in the Capricorn-Bunker Group [Modini et al., 2009]. The reef-produced biogenic aerosols seem to increase in the morning and afternoon periods, possibly regulated by tides [Fischer and Jones, 2012; Jones et al., 2007], with a short discrete peak close to mid-day; coinciding with an increase in atmospheric DMS (DMSa) and production of ammonium sulfate aerosol (a known oxidation product of DMSa) and volatile organics [Modini et al., 2009]. A distinct tidal signature of the build-up of DMSa in the MABL and CARL (during low and flood tides) may significantly influence the radiative environment over reefs causing variations in downwelling solar radiation over such tidal cycles [Charlson et al., 1987]. However, direct measurement of any causal effect of DMS on radiation transfers over coral reefs such as Heron Reef has not been made.
 The periods 540–1100 EST and 1100–1510 EST had similar conditions, with easterly winds at around 3 m s−1 at the surface and an average change in Tair of 0.4°C and 0.3°C, respectively. The total hourly QH was lower during the morning period at 6.7 W m−2 h−1 (Figure 7a), compared to 31.2 W m−2 h−1 during the afternoon when a very low tide occurred (0.2 m), and Tsurf reached >31°C. In addition to higher QH, Q*BL had also increased during the afternoon (1.7 W m−2 h−1, up from 0.5 W m−2 h−1) with an increase in K↓ of 74% yet the total heating rate (QBL) was similar due to Qadv having a stronger influence in the afternoon. Strengthening of the winds above the CARL as indicated by radiosonde ascents (not presented here) may have contributed to the higher Qadv during the afternoon. Due to higher solar radiation, Hsoil was 3.2 times higher than during the morning period, yet Sabs had decreased due to the lower water level. The surplus of heat in the reef flat during this period was flushed from the reef flat via ΔF, which was −80.7 W m−2 h−1 (Figure 7b).
 This study has presented results from a simple thermal heat budget analysis for Heron Reef for a four day period and for the CARL during selected case study days in June 2009 and February 2010. The interrelationships between the thermal budgets, the surface energy balance, and the structure and evolution of the CARL, prevailing meteorology and hydrodynamics have been investigated by using direct in situ measurements of the surface energy balance of the water, the medium through which the water column and CARL interact. It is the first study to examine both the thermal budget of the water column and the overlying atmosphere above a coral reef.
 During both the summer and winter case studies, clear processes of heating and cooling were observed in the CARL and within the water. The heating rate of the CARL was similar in the morning and afternoon periods of 12 February 2010, with relatively uniform heating and QBL. By comparison, the CARL was more stratified during the winter case study on 14 June 2009 and followed a diurnal cycle similar to that observed over land in a coastal setting [McGowan and Sturman, 2005]. This cycle involved a morning cooling period associated with the transformation of a nocturnal stable inversion to an unstable layer, followed by a midday warming phase, and stronger heating in the afternoon as the daytime θv lapse rate became more mixed. Over Heron Reef, this diurnal signal has been shown to be weaker than over land, yet typically stronger during winter than summer due to higher QH and QE, particularly under the influence of cool, dry south-westerly winds that increase the surface-air temperature and moisture gradients [MacKellar et al., 2012b].
 Sensible heat flux at the surface was the key input of energy into the CARL over Heron Reef on both 14 June and 12 February, and was often higher in the afternoon when Tsurf had increased due to high Qwater. This indicated that heating of the CARL lags heating of the water. Radiative divergence had an additional but smaller influence than QH and was higher on 12 February 2010 than 14 June 2009, and was generally higher later in the day. The increase in Q*BL during these times was primarily due to the higher K↓, in addition to an increase in q and potentially atmospheric aerosol, such as DMS. The heat gained due to QH and Q*BL was balanced by cooling due to Qadv during both observation days, highlighting a key temperature regulating mechanism. In contrast to this finding, Qadv has been observed to provide an additional source of heat to the terrestrial boundary layer at valley floor sites where local thermal winds develop during the daytime [Kuwagata et al., 1990]. McGowan and Sturman , however, found that Qadv had a cooling effect on the boundary layer closer to the coast due to onshore flow of cooler maritime air.
 With much of the available solar radiation entering the water during the daylight hours, and owing to the higher specific heat of water compared to air, the heat fluxes in the water were significantly larger than the CARL. Net longwave radiation was consistently negative above the reef and, in conjunction with the heat loss due to the turbulent fluxes, cooled the water overlying the reef. The heating by solar radiation far exceeded this cooling during the daytime, however, with Sabs having a strong influence on water temperature during both observation periods, in addition to Hsoil. Sharp peaks in Qwater and ΔF were observed when the incoming tide occurred in the morning, inundating the reef flat and shallow lagoon (which had cooled overnight) with warmer oceanic water. This was most evident during 11–14 June 2009 when the cooling of the water in the shallow lagoon was exacerbated by high QH and QE, resulting in spikes of ΔF and Qwater when the water level surpassed 1.2 m. This appeared to represent the water level at which enhanced mixing due to the influx of oceanic water across the reef occurred, i.e., the water level was high enough to flood over the reef crest. McCabe et al.  also observed sudden increases in water temperature associated with warm water in the flood tide at Lady Elliot Reef, to the south of Heron Reef. Large ΔF fluxes (>2000 W m−2) were also recorded by Nihei et al. [2002b] in a mangrove swamp (water level 0–0.5 m) at Ishigaki Island, Japan, adjacent to a reef during the incoming tide as warmer water from an adjacent reef flooded the area. Similarly, ΔF decreased during the ebb tide at Heron Reef. Nihei et al. [2002b] observed tidal flushing of the reef at Ishigaki Island (ΔF <−1500 W m−2) during October 2000 subsequent to afternoon low tides when the reef waters were warmest and cooler sea water intrusion resulted in an abrupt decrease in water temperature. During 9–12 February 2010, this process was also evident, albeit to a lesser degree, due to a lower range in water temperature. The daily average Hsoil during February 2010 was approximately twice that of the June 2009 field campaign due to shallower water and higher K↓.
 The energy balance across the water surface is the key medium through which the heat balance of the water column and CARL interact. The primary heat source for the CARL was QH, whilst solar heating (Sabs and Hsoil) and ΔF were the primary heat sources for the water column. Nadaoka et al.  showed that QG and ΔF were the key heat fluxes associated heating and cooling of Ishigaki Reef, Japan, although the radiative processes within the water were not accounted for. The findings of this paper have shown that the temperature of the water over the reef is controlled by interactions between the surface energy balance, radiation transfers, and hydrodynamics (tides and circulation), all of which are influenced by the prevailing weather conditions, including cloud cover, wind speed, Tair, q, and aerosol concentrations.
 The results of these short-term CARL heat budget analyses indicate that the reef flat and shallow lagoons are constant sources of sensible heat to the atmosphere. With the SST around Australia predicted to increase by 1.5–3°C by 2070 [Hobday and Lough, 2011], the flux of sensible heat to the atmosphere is likely to be enhanced, augmenting CRL heating, and influencing regional weather. This may include modification to local wind fields by strengthening the horizontal temperature and pressure gradients across the reef-ocean boundary, similar to those across strong oceanic fronts [Hsu, 1984], as well as cyclone intensification [Krishna and Rao, 2009]. Results also provide insight into local spatial variation in coral bleaching due to thermal and radiation extremes on reef platforms. Patchiness in coral bleaching has been attributed to spatial variation in microclimate and other factors including water flow, species adaptability, exposure to extreme tides, waves, and shading, amongst other biological and physiochemical influences [Davis et al., 2011; Lenihan et al., 2008]. Accordingly, these studies are important for understanding variation in coral physiology and adaptability in a thermally variable environment [McCabe et al., 2010]. Our results indicate that moderation of water temperature due to energy exchanges across the air-sea interface and tidal flushing is inhibited when settled anticyclonic conditions and neap tides coincide. It seems likely, therefore, that these conditions will become more prevalent as the sub-tropical high pressure belt continues to expand [Seidel and Randel, 2007], posing a greater risk of coral bleaching due to higher frequency of above-average temperatures and a decrease in surface wind speeds over sub-tropical coral reefs such as Heron Reef in the southern Great Barrier Reef.
 Given that QSWR, QG, ΔF, Hsoil, and Qadv were all residual components of the various heat budget equations and considering the inherent inaccuracies associated with instrumentation, the derived heat budgets presented here are subject to an inevitable margin of error. Furthermore, the heat budget for the water column can only be considered representative of the geomorphic zones from which the measurements were made. Despite these caveats, the results provide valuable insight into the key physical processes that underpin the thermal state of coral reef environments. They build upon previous work [Davis et al., 2011; McCabe et al., 2010; Nadaoka et al., 2001] by presenting direct measurements of the surface energy and radiation fluxes and accounting for the influence of radiative processes in the water and thermal conduction due to the sea floor and benthic cover, the latter which had a considerable heating effect on the water column. Ongoing research is needed to investigate the spatial variation in the heating rates of the CARL and water column in various geomorphic zones and coral reefs of varying benthic assemblage, and under a wider range of meteorological and hydrodynamic settings. Given that the advective fluxes are such an important factor in moderating the temperature of both the CARL and water column, further investigation is warranted in order to improve our understanding of these processes, particularly as previous research has indicated that this parameter is a key moderator of coral bleaching severity [MacKellar and McGowan, 2010; Anthony and Kerswell, 2007]. This includes parameterization of the various contributions from wave action, wind stress, and bottom stress to the advection flux within the water. Additional measurements of the optical properties and turbidity of the water column would also be valuable in order to examine their potential influence on the heat budget of the water, as well research to accurately quantify the influence of biogenic aerosols on radiation transfers and atmospheric heating. Finally the role of light scattering due to atmospheric aerosol and cloud on atmospheric albedo and the radiation budget should be considered in future work. This should include measurement of the albedo at the top of the CARL in order to improve this initial heat budget analysis.
 Understanding of the physical processes that underpin the thermal environment of coral reefs is crucial for understanding and forecasting the weather and climate of tropical and sub-tropical coastal environments and for facilitating the prediction of how coral reefs and their inhabitants will respond to climate change. It is also essential for providing insight into the spatial variation in coral community structure and coral bleaching intensity. Previous studies have provided insight into the heat budget of coral reef waters, but have suffered from a common lack of direct measurements of the water surface energy fluxes, while the heat balance for the CARL has remained undescribed. Accordingly, this paper presents the first analyses of the daytime heat budget of the CARL, the reef-water surface, and for the water column overlying a coral reef. Heat budgets were calculated using direct measurements of air-sea energy fluxes, atmospheric soundings, and hydrodynamic conditions during 4 day periods in June 2009 and February 2010.
 The results showed that heating of the CARL was the most evident during the winter case study, under anticyclonic conditions, when a clear diurnal cycle of boundary layer evolution was observed over the reef. Accordingly, as the structure of CARL transitioned from stable in the early morning to unstable, followed by a more mixed layer, the CARL underwent considerable heating and cooling. By comparison, under similar anticyclonic conditions during the summer case study, the CARL exhibited more isothermal conditions throughout the day, indicating that turbulent mixing was stronger, resulting in a less pronounced heating and cooling cycle. During windy periods, the air-water temperature gradient increased (e.g., during winter) enhancing the sensible heat flux to the CARL. This increase in CARL heating was dampened by the horizontal advection of heat out of the volume of air over the reef, which had a consistent cooling effect of the CARL during both case study days. Radiative divergence within the layer accounted for only a small portion of heating (although it was higher in the summer time).
 During periods when sensible and latent heat fluxes were high, cooling of the water overlying the reef flat was exacerbated. Sensible heat flux was typically higher during the afternoon periods, however, when radiative heating of the water column dominated over cooling by longwave and turbulent flux exchange. Horizontal advection in the water column was responsible for sudden increases in water temperature, particularly during the winter case study after early morning low tides when the horizontal temperature gradient between the reef and ocean was high and the rising tide inundated the shallow lagoon with warmer water. After commencement of the ebb tide, horizontal advection decreased markedly and had a cooling effect during the afternoon in the summer field study when the low tides resulted in accumulative heating of the shallower water on the reef flat. Future research will involve more comprehensive hydrodynamic measurements, in order to more closely examine the advective fluxes in the water under a wider range of meteorological and hydrodynamic conditions.
 We extend our thanks to the School of Geography, Planning and Environmental Management, The University of Queensland for continued financial and technical support, Glenn Ewels for assistance during field campaigns, and the Great Barrier Reef Marine Park Authority for permitting our research at Heron Reef (Permit G09/3033.1).