Progressive seawater acidification on the Great Barrier Reef continental shelf

Coral reefs are highly sensitive to ocean acidification due to rising atmospheric CO2 concentrations. We present 10 years of data (2009–2019) on the long-term trends and sources of variation in the carbon chemistry from two fixed stations in the Australian Great Barrier Reef. Data from the subtropical mid-shelf GBRWIS comprised 3-h instrument records, and those from the tropical coastal NRSYON were monthly seawater samples. Both stations recorded significant variation in seawater CO2 fugacity (fCO2), attributable to seasonal, daytime, temperature and salinity fluctuations. Superimposed over this variation, fCO2 progressively increased by > 2.0 ± 0.3 µatm year−1 at both stations. Seawater temperature and salinity also increased throughout the decade, whereas seawater pH and the saturation state of aragonite declined. The decadal upward fCO2 trend remained significant in temperature- and salinity-normalised data. Indeed, annual fCO2 minima are now higher than estimated fCO2 maxima in the early 1960s, with mean fCO2 now ~ 28% higher than 60 years ago. Our data indicate that carbonate dissolution from the seafloor is currently unable to buffer the Great Barrier Reef against ocean acidification. This is of great concern for the thousands of coral reefs and other diverse marine ecosystems located in this vast continental shelf system.

recorded for some shallow tropical coastal and shelf marine habitats 21,22 , a variation that is several-fold greater than in the open waters. Given the large temporal and spatial variability and the high ecological and economic value, more long-term carbon chemistry data from coastal and shelf locations are urgently needed.
In this study, we assessed variation and trends in CO 2 and other proxies for ocean acidification from two sites in the Australian Great Barrier Reef (GBR). The GBR is a shallow carbonate rich continental shelf system extending over 2300 km along the north-eastern Australian coast from 12 to 24° S latitude, and varies in width from 40 to > 200 km (Fig. 1). The GBR is an interesting case study for ocean acidification research, due to its complex hydrodynamic and geomorphological features, and its valuable reef ecosystems. About 5% of the GBR surface is occupied by ~ 3000 coral reefs that are built by corals and other calcifying organisms with a strong dependence on the saturation state of carbonate minerals 8,10,22 . Furthermore much of the seafloor between the coral reefs is covered by biogenic carbonate sediments 23 with habitats that include mesophotic coral shoals, Halimeda mounds, seagrass meadows, sponge gardens and soft bottom ecosystems. Spatial and temporal patterns in the carbon chemistry of the GBR seawater are characterised by substantial cross-shelf gradients, with additional regional features along the coast [24][25][26] and in the proximity of coral reefs 22,27,28 . The surface waters flowing from the Coral Sea onto the GBR shelf are low in nutrient and chlorophyll concentrations, but occasional upwelling onto the shelf break can inject nutrients, total alkalinity and dissolved inorganic carbon into the GBR waters 29,30 . Thirtyfive major rivers drain into the GBR lagoon, and their sediment and nutrient loads affect water clarity for months after floods 31,32 . Terrigenous sediments dominate near the mouths of these rivers 33,34 . The ratio of terrigenous to carbonate sediments declines steeply away from the coast, as flood plumes disperse predominantly the fine silts, and storms redistribute terrigenous sediments predominantly within the innermost 15 km of the lagoon 35 .
We present 10 years (2009-2019) of carbon chemistry data together with auxiliary data, from two fixed long-term GBR oceanographic monitoring stations ~ 650 km apart (Fig. 1a, Supplementary Table S1). The first station, GBRWIS 36,37 (− 23.459° S, 151.927° E), is located in the subtropical southern mid-shelf GBR, at ~ 16 m depth in a channel separating the coral reefs of Wistari Reef from those surrounding Heron Island and ~ 20 km from the edge of the continental shelf (Fig. 1b). The second station, NRSYON 38 (− 19.305° S, 147.622° E), is a National Reference Station in the tropical central coastal GBR, located at ~ 26 m depth at the Yongala shipwreck near the Burdekin River mouth. We determined the long-term trend and variation in CO 2 , and identified the main physical and chemical drivers of the observed changes. We assessed commonalities and differences of the two stations, and we hindcast changes over the last 60 years. Despite their contrasting settings and substantial seasonal and diel variation, both GBR stations showed significant and rapid rate of increase in CO 2 , hence it is likely that some biological processes in GBR coral reefs are already affected by ocean acidification.

GBRWIS station.
At GBRWIS, all four instrumental time series showed strong long-term trends, which we refer to in the rest of this paper as the decadal trend. Atmospheric CO 2 increased at a mean rate of 2.00 ppm year −1 ± 0.011 (1 standard error) throughout the 10-year observation period, with only minor seasonal variation (Fig. 2a, Table 1). Mean daily seawater CO 2 fugacity (fCO 2 ) increased progressively by 6.4% of its initial value over the decade (Fig. 2b), at a mean rate of 2.35 ± 0.17 µatm year −1 . The rates of increase in fCO 2 did not differ significantly from that of the atmospheric CO 2 (GLS on monthly averaged data, N = 109, P = 0.69). Mean daily seawater temperature increased slightly throughout the decade by 0.026 ± 0.013 °C year −1 , and there was also an upward trend in salinity at a mean rate of 0.037 ± 0.001 units year −1 (Fig. 2c,d).
Seasonal variation in the daily mean seawater values were high (Fig. 2, Table 1). Daily mean fCO 2 values were on average 67 µatm higher in the two warmest months (January-February: 406 µatm) compared to the two coolest months (July-August: 339 µatm). Seawater temperature varied seasonally by 5.3 °C (27.0 °C versus. 21.7 °C), whereas salinity averaged 35.5 with overall relatively minor systematic seasonal variation, but brief downward spikes that occurred mostly in the wettest summer seasons (Fig. 2d).
Diel variation in fCO 2 often exceeded 50 µatm and at times > 100 µatm, particularly in summer (Fig. 3a). Diel fCO 2 ranges averaged 37 ± 0.71 µatm across the six warmest months (November-April), and 24 ± 0.50 µatm in the six cooler months. Diel ranges in seawater temperature averaged 0.56 ± 0.01 °C and 0.41 ± 0.01 °C in summer and winter, respectively. Overall, mean fCO 2 values were highest during summer nights (midnight to 4 am) averaging 389 µatm (376 µatm in winter nights; Fig. 3b). They were lowest on winter afternoons (noon to 4 pm), averaging 333 ± 0.58 µatm (341 µatm on summer afternoons). Hence mean diel variation in fCO 2 was about 30-50% of the ranges of the mean seasonal variation, and was attributable to changes in temperature and reef metabolism (photosynthetic CO 2 uptake and night respiration).
To determine the relative strength of the estimated decadal trends and the role of co-varying environmental factors, non-hierarchical GLMs and partial dependence plots were used on monthly averaged data. The decadal upward trends in atmospheric CO 2 , seawater temperature and salinity were significant, with very strong effects of month (representing seasonal variation) for temperature and much weaker effects of month for atmospheric CO 2 and for salinity (Table 2a). Seawater fCO 2 also displayed a strongly significant decadal upward linear trend, and additionally it varied with temperature, salinity, and month (Fig. 4, Tables 1, 2b). Thus, after adjusting for the variation in seawater temperature, salinity and months using the GLMs, the decadal trend in fCO 2 remained strong and significant (1.792 ± 0.3612 µatm year −1 , t = 4.960, P < 0.001). The decadal trend was similarly strong for fCO 2 -T, i.e., after temperature normalisation to remove the influence of seawater temperature on the fCO 2 trend following Takahashi et al. 39 , the decadal fCO 2 -T trend was 1.828 ± 0.628 µatm year −1 (t = 5.009, P < 0.001). The strongest predictor for variation in both fCO 2 and fCO 2 -T at GBRWIS was the decadal linear trend (Table 2b).  www.nature.com/scientificreports/ The NRSYON seawater samples showed no overall significant differences across the four sampling depths (Fig. 5b,c), despite some individual samples showing depth differences that suggested occasional weak stratification especially in summer. Based on the absence of systematic depths differences, all data were averaged across depths within sampling months for the following analyses (N = 107).
NRSYON data displayed strong seasonal variation ( Fig. 5b-g; Table 1). fCO 2 values ranged over 113 µatm, being on average 58 µatm higher in the warmest vs the coolest months (402.5 µatm vs 344.3 µatm). Ω ar was also higher (3.76 vs 3.45). Mean seawater temperatures were 6 °C higher during the two warmest compared to the two coolest months (January/February: 28.7 °C, July/August: 22.7 °C), while salinity and pH T were lower in the warmest versus the coolest months. Mean concentrations of dissolved inorganic nitrogen, total phosphorus and silicate were relatively low, however variation was high (Table 1).
Superimposed over the seasonal variation, many of the NRSYON data showed strong decadal trends ( Fig. 5b-g). Measured DIC increased by 3.09 ± 0.67 µmol kg −1 SW year −1 . Calculated fCO 2 increased on average by 2.00 ± 0.92 µatm year −1 , at a rate that was not significantly different from that of the atmospheric CO 2 trend at nearby Cape Ferguson (2.37 ± 0.03 ppm CO 2 year −1 ; GLS, P = 0.69). Calculated pH T declined by 0.00156 ± 0.0009 units, and Ω ar by 0.0044 ± 0.0048 units year −1 . Seawater temperature and salinity also increased over the decade ( Fig. 5f-g).
The statistical analyses showed the decadal upward trends in temperature and salinity to be significant (P < 0.05), albeit only marginally so for temperature (non-hierarchal GLM analyses, also accounting for seasonal variation; Table 3). For DIC, fCO 2 , pH and Ω ar , but not for A T , the decadal trends remained significant after accounting for seasonal variation (months) and changes in temperature, salinity and nutrients (dissolved inorganic nitrogen, phosphorus and silicate) (Fig. 6, Supplementary Fig. S1a,b, Table 3). For DIC and A T , the strongest predictor was salinity, with weaker but significant effects from DIN and month. Calculated fCO 2 , pH, Ω ar and the Revelle factor were most strongly related to temperature, followed by the decadal trend and silicate. After normalisation to mean salinity values following Friis et al. 40 , the decadal trend in DIC-S became weaker  noaa.gov/gmd/ccgg/trend s/), and the means and percentiles for the two warmest (January and February) and coldest months (July and August). Also tabled are the estimated slopes (± standard errors) for the decadal trends derived from non-hierarchal GLM analyses of monthly averaged data (the seawater carbonate data corrected for variation with seasons, temperature, salinity and nutrients; Figs. 4, 6; Tables 2, 3; ns = not significant). *Variables calculated from DIC and A T for in situ temperature, pressure, nutrients and salinity, using CO2Sys 61 with pK1 and pK2 dissociation constants of Dickson and Millero 62 and KHSO4 dissociation constants of Dickson 63 , total borate of Uppstrom 61 and the equilibrium constant for HF from Perez and Fraga 62 . pH T pH at total scale, Ω ar aragonite saturation state, fCO 2 fugacity of seawater CO 2 , bdl below detection limit. Measurements of DIC and A T used for CO 2 system calculations were only available for NRSYON.   Table S1, Fig. 1C). However, salinity remained a significant predictor, suggesting slight over-compensation by the normalisation. Normalisation of fCO 2 to mean temperature also showed that the decadal trend remained significant at 1.259 µatm year −1 ± 0.3696, P < 0.001 (also accounting for changes in salinity, nutrients, and months; Supplementary Table S1). For the nutrients, silicate was significantly associated with all carbon variables except for A T . DIN was significantly associated with DIC and DIC-S and marginally with A T and A T -S. Phosphate was only weakly associated with DIC and DIC-S.
The similarity in the decadal CO 2 trends at both GBR stations to the atmospheric CO 2 changes suggests these CO 2 trends are largely determined by atmospheric forcing, as also found at the open ocean sites. This assumes there has been no significant reorganisation of the biological and physical processes influencing surface water carbon chemistry over the decade of measurements at our two sites. NRSYON is strongly influenced by coastal processes and is close to a major river outflow, but ~ 100 km from the shelf edge, whereas the GBRWIS site is Table 2. GBRWIS: factors related to the observed variation in (a) atmospheric CO 2, seawater temperature and salinity, and in (b) fCO 2 (Fig. 4) and fCO 2 normalised to the local mean temperature (24.34 °C) 39 . Nonhierarchal generalized linear model (GLM) analysis of monthly mean data (N = 109 months).    www.nature.com/scientificreports/ www.nature.com/scientificreports/ located next to a coral reef but 68 km off the coast and within 20 km of the shelf edge and the open-ocean waters of the Coral Sea. The buffering capacity by the carbonate sediments that cover most of the seafloor in the GBR was clearly insufficient to prevent the rapid acidification of the water body near these two stations for the 10-year duration of the measurements. Based on this similarity we suggest the observed decadal trends are unlikely to be exclusive to the two sites and reflect the trend over a broad region of the central and South GBR. Seawater temperature and salinity also showed significant upward trends over time at the two GBR stations, consistent with regional oceanographic and climatological features. The physical oceanography of the GBR is dominated by the inflow of Coral Sea water which bifurcates offshore between about 15 and 20° S, leading to predominantly southward-bound offshore currents, and northward bound inshore counter currents in the southern and central GBR 45 . Sea surface temperatures are increasing over the whole GBR region with changes in Coral Sea source waters of 0.1-0.2 °C per decade 46 . The variable salinity trend is consistent with temporal and regional variation in monsoonal rainfall and river flows, and also reflects slight salinity increases in Coral Sea waters 41 . The climate of Northeast Australia is additionally influenced by ENSO cycles, which typically have a 2-7 years duration. At both sites, El Niño (La Niña) events were associated with anomalously high (low) salinities compared to the long-term trend. La Niña conditions with increased rainfall were present from mid-2010 until about March 2012 47 . By mid-2014, a moderate to strong El Niño with low rainfall emerged and persisted until mid-2016, followed by neutral conditions 48 . At GBRWIS, the downward spikes in salinity coincided with large rainfall events in 2010/11, 2013 and 2019. The coastal NRSYON site had a greater variability and trend in salinity than GBRWIS, likely attributable to its greater exposure to coastal inflows, and the influence of net evaporation or precipitation in shallower water. The Burdekin River had large discharges and northward plume flows in the summers of 2007/08 to 2011/12 and 2018 and 2019 with seasonally low salinities at NRSYON, and low discharges from 2012/13 to 2017/18 that corresponded with higher salinities in the summer wet season at the site.
Both temperature and salinity play an important role in determining changes in the seawater carbon chemistry, directly as temperature determines the solubility of CO 2 and salinity affects A T and DIC, and indirectly as biotic metabolism accelerates with temperature. Total alkalinity at NRSYON was strongly related to salinity, with prolonged reductions in years with high river flows. The decadal increase in temperature and salinity, and resulting changes in A T and DIC at NRSYON will cause an increase in fCO 2 and decrease in pH and Ω ar . However, the decadal upward trend in fCO 2 remained significant after normalisation to a mean temperature at both sites, and also after statistically adjusting for the effects of rising temperatures and salinity. This again confirms the strong role of atmospheric forcing in driving the trends in seawater CO 2 chemistry over the duration of our study. In addition to the decadal trends at both sites, there is substantial seasonal variation in the carbon chemistry due to seasonal temperature fluctuations and biological activity. Longer term observations through multiple ENSO events are needed to resolve the combined influences of local and large-scale controls on the rate of ocean acidification in the GBR more clearly.
We hindcasted fCO 2 conditions in the GBR over the last 60 years, when the longest existing greenhouse gas records commenced at Mauna Loa, Hawaii (since 1958; www.esrl.noaa.gov/gmd/ccgg/trend s/). The decadal Table 3. NRSYON: environmental and temporal factors associated with changes in seawater carbon chemistry variables. Non-hierarchal generalized linear model (GLM) analysis of monthly depth-averaged data (N = 107 months). Tabled are the decadal trend and variation due to seasons (Month) for seawater temperature and salinity, and the decadal trend, seasonality and environmental predictors (seawater temperature, salinity and nutrients) for selected carbon chemistry variables: measured DIC and A T , and calculated fCO 2 , pH, and the Revelle factor (Fig. 6, Supplementary Figure S1a   . The slopes of seawater fCO 2 at GBRWIS and NRSYON over the same time period were also statistically similar, increasing at 2.35 ± 0.17 and 2.00 ± 0.92 µatm year −1 respectively, with an offset by − 26 ppm for GBRWIS and − 13 µatm for NRSYON compared with their atmospheric CO 2 values. Our data suggest that today's fCO 2 minima are likely above the maxima these two sites would have experienced in the early 1960s ( Fig. 7). At NRSYYON, the current (2009-2919) average range of winter to summer fCO 2 is 344.3-402.5 µatm (Table 1) and extrapolation back to 1958 gives a range of about 261-319 µatm, i.e., the current envelope is outside than from 50 years ago. At GBRWIS, only fCO 2 and no other systematically sampled carbon chemistry data are available over the 10-year sampling period, however the present day average winter-summer range of fCO 2 (339.4-405.9 µatm) is also probably outside the average seasonal range in the early 1960s of 333-250 µatm (Fig. 7). Our hindcasts assume that fCO 2 at the GBR sites have tracked the atmospheric increase at Mauna Loa, and that GBR seawater A T has remained similar since 1958. The observed long-term changes in temperature and salinity are too small to alter this result. The increasing Revelle Factor with time due to surface water CO 2 uptake has likely amplified rather than diminished the seasonal signal today relative to that of the 1960s. Factors such as a widespread decline in net calcification on the reef since the 1960s may have altered the fCO 2 ranges by changing A T and DIC concentrations, however few data from before 2009 exist to determine if this is has occurred. Therefore,   (a,b), and the other carbon chemistry variables (c-f) related to decadal trends (date). Trend estimates of are controlled for changes across months and in temperature, salinity and nutrients (Table 3, Supplementary  Fig. S1). Values on the y-axis represent differences from the mean values (Table 1) Variation in seawater fCO 2 , and the role of environmental drivers. Surface seawater carbon concentrations showed substantial seasonal variation compared to the atmospheric CO 2 , likely attributable to seasonal changes in temperature and salinity, to benthic and pelagic production, as well as to differences in source water bodies 25 . However, observed ranges in fCO 2 at the two GBR stations were moderate compared to many other coastal stations 15 . Total ranges were 143 µatm at GBRWIS and 113 µatm at NRSYON, while seasonal ranges averaged 67 µatm at GBRWIS and 58 µatm at NRSYON. Diel ranges were only assessed at GBRWIS, where they averaged 40 µatm in summer and 24 µatm in winter. In comparison, at moorings around O'ahu, Hawai'i (2008-2016), the coastal pCO 2 station in Kaneohe Bay behind a strongly calcifying shallow coral reef with slow turnover and strong terrestrial influences displayed a maximum CO 2 range of 950 µatm pCO 2 , while two other Hawai'ian stations with less calcification exhibited surface water pCO 2 variability ranging from 198 to 240 µatm 21 . Mean diurnal variability at Kaneohe Bay at 192 µatm was also 4-5 times greater than at GBRWIS. In Hawai'i as in the GBR, the seasonal seawater CO 2 dynamics were opposite to those in the atmosphere, with highest seawater CO 2 values in summer and lowest values in winter.
Seasonal variation was greater on the mid-shelf GBRWIS than at the coastal NRSYON (Table 2), and there was a larger mean gradient between seawater and atmospheric CO 2 at GBRWIS compared to NRSYON (26 vs 13 ppm). A comparison between the two stations needs to be done with caution: at GBRWIS the fCO 2 was directly measured by instruments day and night and in all weather conditions but only at about 0.5 m water depth. At NRSYON, fCO 2 was calculated from seawater DIC and A T sampled at four depths through the 26 m water column and samples were only collected during daylight and not in very windy conditions. The subtropical GBRWIS also experiences slightly greater seasonal variation in daylength and temperature compared to the tropical NRSYON, likely contributing to its greater variability. Furthermore GBRWIS is located near shallow and actively calcifying coral reefs, while NRSYON is located near a major river in ~ 26 m deep turbid water without shallow reef structures nearby, and light on the seafloor is low 49 . Consequently, the greater diel fluctuations in fCO 2 in summer than winter at GBRWIS are likely attributable to daytime photosynthesis and night respiration www.nature.com/scientificreports/ being greater at the higher temperatures and higher PAR in summer. Considering all these factors, it appears the biological processes on the coral reefs had a greater effect on the local carbon chemistry around GBRWIS than did the more variable salinity, nutrients, sediments and inter-reefal benthos near the Burdekin River at NRSYON. Seawater nutrient concentrations were positively related to some of the carbon chemistry variables at NRSYON (Supplementary Fig. S1, Table 2). However mean concentrations of dissolved macronutrient are typically low in the tropics except in waters exposed to terrestrial runoff and upwelling, with maximum observed concentrations of phosphate and DIN of 0.24 and 3.8 mmol/kg, respectively (Table 1). River nutrient load data are only available on a yearly basis, so could not be included into the models. However, at this site macronutrient availability did not appear to be a dominant driver of the CO 2 variation on seasonal scales. Overall, concentrations of alkalinity and DIC appear typically lower in Burdekin River discharge waters than in seawater, but they are higher in alkalinity than in DIC 50 . Due to the sparsity of relevant river data and complex hydrodynamics, it remains unclear to what extent rivers affect the alkalinity and inorganic carbon concentrations of GBR ecosystems, either directly through their DIC, alkalinity and nutrient loads, or indirectly via stimulation of biological processes.

Conclusions
We have shown that the carbon chemistry at the two GBR stations has changed rapidly over the last decade, with decadal trends that are consistent across locations. The close tracking of atmospheric and aquatic CO 2 in the GBR suggests that its fCO 2 has increased by about 28% since the early 1960s, and that projections of environmental conditions from large scale-carbon cycle models may be used to track changes in the carbon chemistry within the GBR. Our data demonstrate that ocean acidification is not merely a concern for the future of the GBR. Rather, it is already part of its rapidly changing chemical and physical conditions in the Anthropocene. The potential buffering capacity of the surrounding shallow carbonate seafloor in this continental shelf system, and the dynamics caused by the metabolism on its coral reefs and its large rivers, are ineffective in protecting this vast system from ocean acidification based on the ~ 10 years of data we analysed. Seawater fCO 2 concentrations in the GBR are now outside the envelope the GBR experienced in the 1960s, and trends are expected to continue and even accelerate throughout this century, due to the increasing Revelle factor 51,52 .
The implications of this pervasive and rapid change in the concentration of a biologically highly active parameter together with seawater warming, will greatly depend on the location of potential refugia from ocean acidification (if any), and CO 2 emission trajectories. A large number of experimental and in situ studies around volcanic CO 2 seeps have demonstrated the profound implications of ocean acidification for the ecological integrity of coral reefs, including reduced coral calcification, coral biodiversity, coral recruitment, structural complexity, reef accretion rates, and coralline algal cover, and increasing seagrass and macroalgal cover 8,9,53 . Today's mean Ω ar at NRSYON (3.59, down from a predicted historical mean value of ~ 3.92 in the 1960s) is near the measured tipping point of Ω ar = 3.5 to 3.6 for the GBR, at which level crustose coralline algae and the densities of coral juveniles steeply decline and macroalgal cover increases 10 . Eyre, et al. 16 also concluded that the GBR is close to a tipping point when dissolution of carbonate sediments on coral reefs exceeds its generation. Although our data do not support the notion that the carbon chemistry trends at the two sites are modified as yet by net dissolution, longer term records and more measurements in the proximity of benthos are needed to assess this concern. Indeed, the contrasting setting of these stations is valuable in assessing whether or not the GBR is tipping towards conditions of net dissolution. Our study involved only two sites in the south and central GBR, and more data are needed from along its 2300 km length to characterize in greater detail how conditions are changing over time in the broad range of GBR environments (coral reefs, coastal regions including mangroves and estuaries, seagrass meadows and inter-reef regions).
The ongoing support for a global network of fCO 2 and carbon chemistry monitoring sites will remain essential to improve predictions of regional seawater conditions and their drivers. Our data complement other studies 54,55 that show that ocean acidification driven by CO 2 uptake from the atmosphere, together with the rapid increases in global temperatures, is an immediate concern for the persistence of healthy ecosystems in the GBR, rather than a future problem. The data further contribute to the resounding scientific call for immediate and drastic global cuts in CO 2 emissions, combined with strong local management action, to protect coral reefs into the future.

GBRWIS station.
Concentrations of CO 2 in the air (ppm) and surface seawater fugacity of CO 2 (fCO 2 , µatm), temperature (°C) and salinity data were sourced from GBRWIS Station, located in 16 m water depth in a channel between Heron and Wistari Reef, near the eastern side of Heron Island, southern GBR on the mid-shelf (− 23.459° S, 151.927°E; Fig. 1a,b). This CO 2 Acidification Mooring surface buoy is part of the Australian Integrated Marine Observing System (IMOS) National Mooring Network, maintained by CSIRO, Hobart 36,37 , with newly calibrated sensors deployed every ~ 6 months. Surface water and atmospheric CO 2 are measured on either a 2-or 3-h measurement cycle using a Battelle Seaology pCO 2 monitoring system (MApCO 2 ), while temperature and salinity of the surface seawater and the equilibrator are measured with a Seabird Scientific SBE16plusV2. The CO 2 measurement uses a bubble equilibrator with an intake at about 0.5 m depth. Air from the equilibrator headspace is circulated through a LI-COR 820 non-dispersive infrared detector (NDIR) 56,57 and a two-point calibration is automatically conducted before every seawater and air CO 2 measurement, using a zero CO 2 gas (air cycled through a soda lime chamber to remove CO 2 , a nafion drier surrounded by silica gel to remove water vapour) and a CO 2 -in-air span gas (500-550 µmol/mol, prepared by the NOAA Earth Systems Research Laboratory and calibrated on the WMO X2007 scale with a standard deviation of 0.06 µmol/mol; https ://www.esrl.noaa. gov/gmd/ccl/airst andar d.html). Data from 9/10/2009 up to 12/03/2019 were quality-controlled delayed-mode sourced from the Australian Ocean Data Network (https ://porta l.aodn.org.au/searc h), those to 13/10/2019 were  (Fig. 1a,c). The Burdekin River is the largest river entering into the GBR, with annual mean discharges of 7600 GL freshwater, 4.7 million tons of fine sediments, and 9000 tons of particulate nitrogen 33 , causing significant intra-and inter-annual variability in salinity, nutrients and turbidity 31  /NO 2 ), total silicate and total phosphorus were immediately filtered, and measured spectrophotometrically (metadata: https ://catal ogue-imos.aodn.org. au/geone twork /srv/eng/metad ata.show?uuid=fa93c 66e-0e56-7e1d-e043-08114 f8c1b 76). Temperature data were compiled from data loggers maintained at the station 37 .
Data of DIC, A T , temperature, salinity and nutrients were used to compute the other seawater carbon chemistry variables (aragonite saturation state Ω ar , pH at the total scale (pH T ), fugacity and partial pressure of CO 2 (fCO 2 and pCO 2 ) and the Revelle factor) for observed in situ temperature, pressure, nutrients and salinity, using CO2Sys 61 , with pK1 and pK2 dissociation constants of Dickson and Millero 62 and KHSO 4 dissociation constants of Dickson 63 , total borate of Uppstrom 61 and the equilibrium constant for HF from Perez and Fraga 59 . For consistency with the GBRWIS fCO 2 data, our reporting of NRSYON CO 2 trends focused on fCO 2 . Data points with salinity < 34 PSU were removed for the trend analyses (12 of 432 points). Despite significant depth differences on several days, there were no significant overall differences across the four sampling depths, hence all data were depth-averaged to monthly mean values (N = 107). Data on DIC, AT and fCO 2 data are first presented as observed at in situ temperature and salinity values.
Greenhouse gas monitoring station Cape Ferguson. Regional data of atmospheric CO 2 concentrations as dry mole fractions were sourced from the greenhouse gas monitoring station Cape Ferguson (− 19.2773° S, 147.0587° E, central GBR, ~ 30 km from NRSYON; Fig. 1a). Since May 1991, triplicate discrete air flask samples have been collected monthly at this AIMS jetty, during times when winds were onshore (60°-160°) to minimise land influences . Samples are analysed by CSIRO Oceans and Atmosphere, Climate Science Centre-GASLAB, and provided through the World Data Centre of Greenhouse gases, https ://gaw.kisho u.go.jp/searc h/stati on#CFA. Statistical methods. Statistical analyses were conducted in R v3.4.3 (R Development Core Team 64 ), and included the R libraries 'chron' , 'doBy' , 'nlme' , and 'car' . Analyses of linear trends over the 10-years observation period were based on non-hierarchal generalized linear models (GLMs), with predictors based on date (to estimate the decadal trend), temperature, salinity and month (as chronological factor, to account for other seasonal changes such as irradiance or productivity). Since the focus of this study was on long-term trends rather than short-term fluctuations, the data were averaged within months. For NRSYON, the predictors also included dissolved nutrients (total silicate, total phosphorus, and dissolved inorganic nitrogen as the sum of nitrate and ammonium). Dissolved inorganic nitrogen was fourth-root transformed to approximate normal distribution, while the other variables approximated normal distribution. Estimates of trends in temperature and salinity were based on Gaussian GLMs using the decadal trend (date) and months as the predictors. Model effects were mostly additive, except when indicated. Partial dependence plots were used to show the effects of each predictor on the responses while holding other predictors constant at their mean values (or their respective categorical values) 10,65,66 . To provide comparison with more traditional non-statistical DIC, A T and fCO 2 data presentation, the trends analyses were also shown on salinity-normalised DIC and A T values (DIC-S, A T -S) following Friis et al. 40 (mean salinity GBRWIS: 35.49,NRSYON: 35.29), and on temperature normalised fCO 2 (fCO 2 -T) following Takahashi et al. 39 (mean seawater temperature GBRWIS: 24.34 °C, NRSYON: 25.81 °C). The results were almost identical to those from the non-hierarchal GLMs as the latter investigate the contribution of each factor while simultaneously controlling for the effects of all other factors included in the models.
We hindcasted the carbonate chemistry of the two data series to 1958, based on the assumption that GBR A T values, and the slopes and offsets between our GBR data and the data from Mauna Loa since 1958 (www.esrl. noaa.gov/gmd/ccgg/trend s/) have remained similar. To do so, we calculated the slopes and offsets for the current Scientific Reports | (2020) 10:18602 | https://doi.org/10.1038/s41598-020-75293-1 www.nature.com/scientificreports/ (2009-2019) mean fCO 2 winter minima and summer maxima for both stations and the annual mean Mauna Loa (Table 1), and used these offsets to approximate past fCO 2 envelopes at the stations.