A century of change in the California Current: upwelling system amplifies acidification

Domain: earth_science
Published: 2025-11-13
Editorial outcome: minor_revision

Abstract
Predicting the pace of acidification in the California Current System (CCS), a productive upwelling system that borders the west coast of North America, is complex because the anthropogenic contribution is intertwined with other natural sources. A central question is whether acidification in the CCS will follow the pace of increasing atmospheric CO2, or if climate effects and other biogeochemical processes will either amplify or attenuate acidification. Here, we apply the boron isotope pH proxy to cold-water orange cup corals to establish a historic level of acidification in the CCS and the Salish Sea, an associated marginal sea. Through a combination of complementary modeling and geochemical approaches, we show that the CCS and Salish Sea have experienced amplified acidification over the industrial era, driven by the interaction between anthropogenic CO2 and a thermodynamic buffering effect. From this foundation, we project future acidification in the CCS under elevated CO2 emissions. The projected change in pCO2 over the 21st century will continue to outpace atmospheric CO2, posing challenges to marine ecosystems of biological, cultural, and economic importance.

Introduction
Since the beginning of the Industrial Revolution, the oceans have absorbed approximately a third of anthropogenic CO2 emissions, corresponding to an acidity increase of 25% and a 0.1 decline in pH in the open surface ocean1,2. While most open ocean surface waters equilibrate with atmospheric CO2, the magnitude of acidification in coastal regions can be complex due to the combination of both anthropogenic and natural sources of acidity, particularly at depth. For example, in the California Current System (CCS), the eastern boundary current off the west coast of North America (Fig. 1a), intense, episodic coastal upwelling of low-pH, high-pCO2 waters is driven by alongshore winds and associated Ekman transport3,4. As a result, the CCS and adjacent waterways, such as the Salish Sea in the Pacific Northwest, represent a leading edge of ocean acidification (OA) impacts while also providing a window into future ocean conditions and processes. Understanding the impact of ocean acidification in this upwelling system is particularly critical, as the associated delivery of nutrients from the deep ocean fuels one of the most biologically productive and economically vital ecosystems in the world5. Even though organisms in the CCS have historically been exposed to acidified and variable conditions, a synthesis of several studies suggests that many regional species are sensitive to OA6. Despite its importance and potential vulnerability, the trajectory of future acidification in this upwelling system remains unclear due to the interplay of processes that impact regional biogeochemistry.

A central question is whether acidification in the productive CCS will follow the pace of increasing atmospheric CO2, or if dynamical climate effects or other processes will act to either amplify or attenuate acidification. Processes that can modulate acidification in the CCS include changes in upwelling dynamics, shifts in the source of upwelled water, and changes in the amount of exported material from the surface ocean that is remineralized along upwelled isopycnals (Fig. 1b). Recent research has also brought attention to thermodynamic buffering effects that amplify the impact of this remineralization on seawater pH and pCO2 when water masses accumulate anthropogenic carbon (Fig. 1c). This thermodynamic effect highlights the vulnerability to acidification in carbon-rich waters due to low buffering capacity.

Unfortunately, current studies using coupled ocean-atmosphere models and wind stress analyses differ on the predicted sign and magnitude of changes to the mean state and variability of the CCS in the past and future7–18. Furthermore, while the effects of thermodynamic buffering have long been acknowledged and attempts have been made to calculate the impact of changing oceanic carbon buffering capacity19–21, their implications have only recently been applied to evaluate spatial patterns and rates of OA22–25. Given the wide range of results in the literature, the role of climate effects and their interplay with biogeochemistry in a changing CCS remains uncertain. Testing these predictions and resolving long-term trends from natural decadal variability requires observational data that extends beyond the limited range of instrumental records to span longer timescales.

To address this knowledge gap, we reconstruct carbonate chemistry along the US West Coast and Salish Sea over the industrial era (1890–2020) through measurements of boron isotopes (δ11B) in the preserved aragonite (CaCO3) skeletons of Balanophyllia elegans, a common cold-water coral (“Methods” section). To quantify the magnitude of acidification over the past century, we compare historic museum specimens that grew during the Industrial Revolution (1890s) with modern (2020) corals collected from the same locations (“Methods” section, Supplementary Fig. 1). To attribute the geochemical signals to oceanographic processes and predict future conditions, we contextualize the coral record with a biogeochemical regional ocean modeling system (ROMS). We compare both geochemical and modeled acidification signals to a baseline level of acidification, which we define as the magnitude of acidification associated with the uptake of atmospheric CO2 over the industrial era, to assess whether coastal processes attenuate or amplify acidification from CO2 invasion. We analyze acidification in terms of pCO2 as opposed to pH, allowing us to directly compare magnitudes of acidification independent of background carbonate chemistry. Our study builds on the foundational work of Feely et al.26 and Fassbender et al.24 that described key processes, and extends this analysis through time, permitting us to disentangle process-specific signals obscured in short-term records and resolve their impact on carbonate chemistry controls in the CCS over the 20th century.

Results
A century of acidification in the Salish Sea
Focusing first on the primary geochemical record in the Salish Sea, we find that the mean δ11B of modern corals is significantly lower than the mean of historic samples from the same locations (p=<0.001; Fig. 2). We translate the measured decrease in coral δ11B into implied changes in carbonate chemistry over the last 130 years using a high-precision δ11B calibration from lab-cultured corals of the same species27 (“Methods” section). Because our culture calibration and analogous research in tropical corals28 show that coral δ11B is sensitive to both pH and dissolved inorganic carbon (DIC), we present the way that δ11B constrains seawater carbonate chemistry as a line in pH (total scale) vs. DIC space (Supplementary Fig. 4, “Methods” section Eqs. 1 and 2). The pH-DIC lines described by our coral data in Supplementary Fig. 4 are nearly parallel with the contour lines corresponding to specific seawater pCO2 values, which means we can make robust estimates of changes in pCO2 over the past century (hereafter denoted Δ: ΔX=Xmodern–Xhistoric) in the Salish Sea regardless of the process causing the shift in ocean chemistry or changes in DIC (“Methods” section). The coral record indicates that pCO2 increased by 172±41 µatm between the 1890s and 2020, exceeding the rise in atmospheric CO2 of 120 ppm over the same time period (1900–2020). The implied pH change over the industrial era is −0.095 (standard error of the difference between Salish Sea historic and modern = 0.025). If the acidification in the Salish Sea followed the pace of atmospheric CO2 (our baseline case), ΔpH would be only −0.06 (“Methods” section). The pCO2 and pH signals from the coral records indicate that the Salish Sea experienced amplified acidification over the 20th century. Even though the Salish Sea has naturally low pH and high pCO2 and is a net source of CO2 to the atmosphere, our coral records imply that these highly acidified waters not only became even more acidified over the last 130 years, but exceeded the magnitude of acidification implied by atmospheric CO2.

To further interpret our record in terms of absolute pH, we align the modern corals with nearby modern observational data, which are offset by −0.1 (“Methods” section). We attribute this difference to culture conditions described in Gagnon et al.27 to establish the δ11B calibration, which do not exactly match the natural wild coral setting (Supplementary Methods 1.3). This does not affect the interpretation of data from the Salish Sea, where we have historic-modern pairs, but applying this same offset to all coral samples anchors the historical West Coast coral data so they can be compared to modeled historic values and other proxies.

While different oceanographic processes influence the Salish Sea and CCS, the Salish Sea represents an extension of the CCS because the Salish Sea deep waters are sourced from upwelled water masses of the northern CCS. Therefore, our coral record serves as an indirect indicator of general shifts in seawater chemistry of the CCS. As an additional, independent test for amplified acidification across the CCS and in the Salish Sea, we complement our coral data with an evaluation of processes that influence estuarine acidification (Supplementary Discussion 1.1) and a modeling approach. Using an eddy-resolving physical-biogeochemical ROMS that extends along the CCS, we conducted two hindcast simulations spanning 1891–1904 and 1994–2007, hereafter referred to as historic and modern simulations, respectively (“Methods” section). These ROMS model datasets were compared to corals from the West Coast (discussed below) and were also used to set the composition of upwelled water entering a box model of the Salish Sea, which is not resolved in the ROMS model (Supplementary Discussion 1.2). To account for the temporal offset between the modern model (1994–2007) and modern corals (2020), during which additional atmospheric carbon accumulation occurred, we augment modeled pCO2 from 2007 to 2020 to match the collection date of the modern corals (Supplementary Discussion 1.2). The Salish Sea box model approach predicts that seawater pCO2 increased by 185±15 µatm between the 1890s and 2020, agreeing with the magnitude of ΔpCO2 reconstructed using corals. Both the box model and our Salish Sea corals reveal a larger ΔpCO2 than that implied by atmospheric ΔCO2 and support amplified acidification in this region.

Amplified acidification in the California Current System
We then expanded our analysis of historic acidification to the broader CCS using the same hindcast ROMS simulations. While the complex physics captured by the model results in spatial heterogeneity as in the real ocean, robust patterns in the depth structure of acidification are evident (“Methods” section, Supplementary Fig. 7). The well-ventilated upper 25 m of the nearshore CCS (<100 km) show 20th-century changes in the carbonate system that closely track the atmospheric increase in CO2. Below this surface mixed layer, pCO2 changes outpace the atmosphere, indicative of amplified acidification. Averaging the CCS across 50–200 m depth, the ocean has outpaced the atmospheric pCO2 rise by 50%. The magnitude of ΔpCO2 increases with depth below 25 m, reaching a maximum at 100–125 m (Supplementary Fig. 8).

To assess the accuracy of the historic model, we introduce a record of pCO2 based on skeletal δ11B of B. elegans along the US West Coast (“Methods” section, Supplementary Tables 3, 4). Our coral record presents general patterns and trends of acidification that are consistent with modeled predictions in the upper ocean. Below 50 m, every coral record suggests that the magnitude of 20th-century acidification has matched or exceeded the rise in atmospheric CO2. The corals demonstrate that the CCS has indeed experienced amplified acidification over the industrial era, and even capture the trend of stronger amplification of acidification with depth.

In addition to these overall trends, it is worth noting specific differences between coral records and model simulations. For instance, the corals at several locations collected between 100 and 125 m outpace modeled ΔpCO2, suggesting even more amplified acidification. Our coral data from the Santa Barbara Basin (SBB) deviate most from the model and indicate an even lower historic pCO2 than that represented in the model, and thus a larger relative increase in pCO2 (Fig. 3; n=5). Notably, one of the only previously published records of SBB carbonate chemistry over the industrial era also indicates lower historic pCO2 like our historic corals29 (Supplementary Discussion 1.4). Although our data from this region are too sparse to be conclusive, it is possible that regional processes that amplify acidification in the SBB even more than the rest of the CCS are not captured in the model and warrant further investigation.

Overall, the coral record reproduces broad patterns of acidification in the biogeochemical model, and they collectively suggest that the CCS has experienced amplified acidification over the 20th century. To probe potential drivers of this acidification, we test for shifts in upwelling and biological activity over the past century using the ROMS simulations (“Methods” section). A climatology of modeled upwelling velocity suggests that upwelling has weakened slightly during the summer months and its onset has shifted earlier in the year over the 20th century. Comparing 7-year averages of upwelling velocity between the historic and modern eras, the decline in the CCS is statistically significant but only represents a 2% change in strength and is unlikely to have driven the observed amplification of acidification (“Methods” section). Changes in the biological pump could also affect the integrated impact of remineralization on DIC. We quantified this change in integrated remineralization using apparent oxygen utilization. Over the 20th century, changes in remineralization can account for 15% of modeled ΔDIC in the CCS on average, but cannot explain the driving force of amplified acidification (Supplementary Fig. 9).

Much of the amplified increase in pCO2 that we observe in the CCS can be explained by thermodynamic buffering effects. The isopycnals corresponding to upwelled water masses outcrop at open ocean locations, distant from the CCS. Here, we assume that water masses interact with the overlying atmosphere such that initial pCO2 follows increasing atmospheric pCO2. After subduction, remineralization increases DIC, pCO2, and acidification as the water circulates along an isopycnal and is eventually upwelled in the CCS. Increasing initial preformed DIC in response to rising atmospheric pCO2 has an outsized effect on pCO2 and pH in upwelled water due to a reduction in buffering capacity, even if remineralization and circulation rates remain the same (Fig. 1c). This amplification highlights the need to assess rates of acidification with careful consideration of the mean state of the carbonate system, especially in extreme domains in carbonate chemistry space, such as high-carbon upwelling systems. While local physical and biogeochemical factors in other upwelling systems may exert additional influences, the chemical principles underlying the amplification are inherent to all upwelling regimes, underscoring the global implications of this chemical non-linearity.

Averaging across the CCS, estimates of ΔDIC derived from equilibration of atmospheric CO2 at outcropping regions and accompanying thermodynamic buffering effects (“Methods” section Eq. 4) can explain the modeled ΔDIC to within ±15% relative error (“Methods” section, Supplementary Fig. 10). This analysis shows that atmospheric CO2 and thermodynamic buffering effects drive the magnitude of acidification in large areas of economic and ecological value. The remaining residual leaves room for second-order effects such as shifts in upwelling strength and remineralization rates, as described above. Notably, this analysis also underscore the importance of water mass age when attributing biogeochemical change to anthropogenic carbon (“Methods” section). Given the rapid increase in atmospheric CO2 over the past 50 years, considering water mass age in upwelling regions markedly changes the accumulation of anthropogenic carbon, as deeper, older water was in contact with its contemporary atmosphere less recently30. Acidification in the CCS lags the imprint of modern atmospheric CO2 due to water mass age, suggesting that acidification will continue to amplify and worsen in the coming decades.

Predicting future OA in the California Current
Our historic coral data build confidence in the patterns and magnitude of acidification produced by our model, including amplified acidification. From this foundation, we analyze projections for future acidification in the CCS under the representative concentration pathway 8.5 (RCP 8.5). Although RCP 8.5 represents a high-forcing scenario, there is value in bracketing the upper end of potential future states31. These analyses build on a multi-resolution model study that assessed the value of resolving coastal processes in predicting future change15. Amplified acidification is projected to continue in the subsurface CCS throughout the 21st century (Fig. 4d, e). Ominously, ΔpCO2 in the CCS is estimated to continue to outpace the atmospheric rise in CO2 in the coming century by 20% between 50 and 75 m and 60% between 100 and 150 m. pH is expected to decline by –0.30 below 50 m, equivalent to the predicted change for the global surface ocean32. While comparable in magnitude to ΔpH, the increase in hydrogen ion concentration [H+] in deeper waters is nearly double that at the surface because of the logarithmic nature of the pH scale33. The CCS is projected to experience low aragonite saturation states (Ω<1) and absolute pH levels as low as 7.5 at 75 m due to the already highly acidified conditions of the CCS. Local marine organisms of economic, cultural, and biological importance are predicted to experience significant physiological challenges in response to the increasingly acidified conditions6. For instance, Dungeness crab, the largest US West Coast fishery by revenue, is expected to experience reduced growth and survival in early life stages as acidification progresses6,34. While the surface ocean across the model domain largely followed atmospheric CO2 over the 20th century, surface ΔpCO2 lags the atmospheric increase in the 21st century, indicative of the surface ocean’s limit in mitigating the accumulation of atmospheric CO2 (Fig. 4e). Acidification of this magnitude is predicted to have profound impacts on ecosystems of the CCS in the 21st century.

Methods
Sample measurements: sample collection
Historic samples of Balanophyllia elegans (B. elegans) were collected live by the R/V Albatross between 1888 and 1894, and by Ernest Harrison Quayle in 1932. All historic samples were archived in the Smithsonian National Museum of Natural History (Supplementary Fig. 1, Supplementary Data 1). Samples were dried upon collection and archived dry following Smithsonian preservation guidelines. In the Salish Sea, a total of n=13 historic corals were collected from five sites. A total of n=41 historic corals were collected along the outer US West Coast from 10 sites that span from Vancouver Island, British Columbia, to the Channel Islands, California. These corals were collected in the 1890s from sites that would coincidentally become the major federal marine sanctuaries of the US West Coast.

Modern corals (n=42) were collected from the same locations as the historic corals in the Salish Sea aboard the University of Washington R/V Rachel Carson in Fall 2020 (Supplementary Fig. 1, Supplementary Data 1). These corals therefore reflect conditions from approximately 2010 to 2020.

While the collection dates of most coral locations are known, and all corals were living, the age of each coral is unknown. The age of the historic coral at the time of collection is unlikely to affect the study outcome, as pH values were assumed to be relatively stable. Additionally, all of the historic corals in the CCS were collected within 1.5 years of each other (September 1888–March 1890). The age of the modern corals is also unlikely to impact the modern pH values, as they represent conditions over a narrow time window (5–10 years). Any uncertainty in the exact age, and therefore presumed pace of acidification over this period, is within the measurement error of the corals.

Sample measurements: boron isotope analysis
Skeletal sections of ~5 mg CaCO3 were sampled along the primary growth axis from each coral using a Dremel tool approximately ~0.5–1 cm deep. The sampling scale is large relative to skeletal microstructures like centers of calcification, which likely means that their effects are averaged out and homogenized within the bulk sample. This is supported by the systematic trends and tight precision of even smaller samples from Gagnon et al.27. Additionally, the Gagnon et al.27 calibration suggests that intraspecies variability is small compared to environmental effects. The collected material from each coral represents an average over the entire growth period of the coral. It has been estimated that the average life span for B. elegans in the California Current is 6.5–11 years35. This time window is sufficiently narrow that any secular change in pH due to acidification within this period is within the measurement error of the corals. By sampling along the whole primary growth axis, we assume that different coral skeletal components are evenly represented in each sample.

The skeletal subsamples were then analyzed for their boron isotope composition (δ11B) in the St Andrews Isotope Geochemistry laboratories (STAiG) of the University of St Andrews, UK. Samples were first rinsed with ultra-pure water (Milli-Q, 18.2 Ω) and subsequently oxidized to remove any organic fractions using 1% H2O2 buffered with 0.1 M NH4OH at 80 °C following routine sample preparation protocols for boron isotope analyses (e.g., Rae36). Historic samples were dried upon collection and archived dry following Smithsonian preservation guidelines. All samples of the same weight (~5 mg) were treated identically during cleaning to minimize the risk of preferential dissolution of specific coral skeletal components biasing results. Clean samples were dissolved in distilled 0.5 M HNO3 with the aid of ultrasonication. A small aliquot of the dissolved sample (<10% volume) was measured on an Agilent 8900 Triple Quadrupole ICP-MS to determine the boron content in the sample along with major, minor, and trace element composition. The rest of the dissolved sample was separated from the carbonate matrix on an Amberlite IRA 743 boron-specific anionic exchange resin37,38, following the batch protocol of Trudgill et al. 202439. Purified boron solutions were spiked with HF to aid boron washout and measured in a 0.5 M HNO3 + 0.3 M HF matrix40,41 on a Thermo Scientific Neptune Plus MC-ICP-MS equipped with an HF-resistant sample introduction kit and 1013 Ω resistors (see Crumpton-Banks et al.42 for further details). Instrumental mass bias was corrected by standard sample-bracketing with a 15 ppb NIST SRM 951 solution. Total procedural blanks contained <20 pg B (n=4), and hence were negligible against the typical sample size of ~20 ng B (<0.1%). Full procedural uncertainty was assessed using repeat measurement of NIST RM 8301 (Coral) consistency standard run during this analytical campaign, yielding an average value of 24.28±0.12‰ (2SD, n=8) that is consistent with long-term lab reproducibility and interlaboratory reference values43 (24.17). Skeletal data are summarized in Supplementary Data 1.

Data processing: the boron isotope-pH proxy
Paleoproxies provide an invaluable tool to reconstruct historic ocean conditions and contextualize current climate change. Stable boron isotope ratios (δ11B) are recorded in the skeletons of marine calcifiers such as corals, which function as time capsules of past carbonate system chemistry44. We utilized this method to reconstruct the historic state of the CCS through measurements of Balanophyllia elegans, a common cold-water orange cup coral that spans a wide geographic range from Southern Alaska to Baja California.

To test the null hypothesis that δ11B of borate ion has not changed over the past century in the Salish Sea, we conduct a two-sample t-test to determine any difference between historic and modern δ11B. Averaging data across sample locations in the Salish Sea (Supplementary Methods 1.1), there is a significantly higher δ11B in the historic corals (M=24.94, SE=0.10) compared to δ11B measurements from modern corals (M=24.52; SE=0.06); t(63)=3.53, p=<0.001. Assuming that the physiology of coral calcification incorporated in the coral skeletons has not changed over the past century, we conclude that the δ11B of seawater has declined as a result of declining seawater chemistry (Supplementary Fig. 2).

Data processing: coral-based estimates of pCO2 in the Salish Sea
We then translate the coral data into constraints on past seawater carbonate chemistry to add meaning to this measured Δ(δ11B) (Δ= modern–historic). In a previous study, the same species of corals (B. elegans) was cultured under controlled conditions to produce a calibration curve that links skeletal δ11B and seawater pH, the predominant metric to assess ocean acidification27 (Eq. 2). The same culture study also uncovered a subtle but significant relationship between skeletal δ11B and dissolved inorganic carbon (DIC), even at constant pH27 (Eq. 1).

δ11Bcorrection = DIC × 2.5 mmol/kg × 1.08 (1)

pH = (δ11Bmeasured + 1.08 × DIC + 7.2) / 4.33 (2)

Albeit minor relative to the skeletal δ11B–pH relationship, the impact of DIC on skeletal δ11B is nonetheless considered in our interpretation of the coral data (Eq. 2). Because two environmental parameters exert control on δ11B, we explore the coral record in pH vs. DIC space as shown in Supplementary Fig. 4. Historic and modern skeletal δ11B measurement averages are indicated by lines in this space. Fortuitously, we find that δ11B provides a tight constraint on pCO2 regardless of changes in DIC, as can be seen on these plots. Over a large range of DIC values, lines of constant δ11B are nearly parallel with the contour lines corresponding to specific seawater pCO2 values (Supplementary Fig. 4). While individual contours are parallel between pCO2 and δ11B over a wider range of DIC values, the spacing between contours does change subtly with absolute DIC. However, the effect of DIC falls within the measurement error and was not found to have a meaningful effect. Once a rough DIC is established for the modern ocean at coral collection locations from observational (bottle) data, the ΔpCO2 between historic and modern eras is simply the distance in space between the modern and historic constant δ11B lines. Note that DIC does not need to be known well, as it is just used to generally indicate the region of carbonate system space for making the plots used here.

We use climatological means of bottle data from the Washington Ocean Acidification Center cruises to obtain modern values of mean DIC and pH at the sites of coral collection45 (Supplementary Methods 1.2). Most of our Salish Sea coral samples were collected near Admiralty Inlet, a narrow channel at the eastern terminus of the Strait of Juan de Fuca through which most of the seawater that fills Puget Sound flows. Tidal mixing over a shallow glacial sill leads to similar seawater properties through much of the water column at Admiralty Inlet, meaning the properties are generally homogeneous with depth. Climatologies of modern carbonate chemistry parameters for Admiralty Inlet at the coral collection depth of 70 m were generated from several years of bottle data. There is a seasonal pattern of low TA and DIC during the winter months, followed by high TA and DIC during the fall (Supplementary Methods 1.2; Supplementary Fig. 13).

We conducted a sensitivity analysis using both annual and summertime (JJA) averages for modern DIC and found only a minor difference in our reconstructed ΔpCO2 results for the Salish Sea. This is in part because summer and annual climatological means of pH averages are approximately equivalent in the Salish Sea. Armed with this constraint on typical DIC, we can make robust estimates of ΔpCO2 in the Salish Sea regardless of the process that drives the 20th-century change (ΔpCO2 = 172 µatm; standard error of the difference between modern and historic = 41 µatm). We also tested the sensitivity of our pCO2 calculations by conducting a sensitivity analysis on our pCO2 calculations. Temperature values were based on summertime averages from bottle data collected at the Washington Ocean Acidification Center (WOAC) station 21 (Supplementary Table 1), located near a majority of coral sampling sites. Under the assumption that temperature remained constant over the past century, we calculated ΔpCO2 = 172 µatm. However, if we assume that historical temperatures were 1 °C cooler, then ΔpCO2 increases slightly to 176 µatm. This small temperature effect is well within the uncertainty range of the coral records (±41 µatm). Furthermore, if temperatures have indeed warmed over the past century, our acidification estimates would be even larger and more extreme. We adopt a conservative approach and assume a constant temperature over the past century, and thus report ΔpCO2 = 172 µatm in the Salish Sea.

Data processing: coral-based estimates of pH in the Salish Sea
The modern observational data provides additional information that we can use to better calibrate our proxy and to estimate ΔpH for the Salish Sea. Comparing modern observational DIC and pH data (red circle, Supplementary Fig. 4, Supplementary Methods 1.2) to modern δ11B (gray line, Supplementary Fig. 4), we found that a pH offset of −0.10 was necessary to align the two datasets. We attribute this difference to culture conditions not exactly matching the natural wild coral setting. To calibrate the coral data, we apply this pH offset of −0.10 to all our coral data, including our historic and modern records from the Salish Sea and historic records from the US West Coast. This offset does not impact the interpretation of data from the Salish Sea, where we have historic-modern pairs, but applying this same offset to all coral samples anchors the historical West Coast coral data so they can be accurately compared to modeled historic values and other proxies. We also find that the summer and annual climatological pH averages are approximately equivalent in the Salish Sea, so applying an offset informed by the observational summertime average instead of choosing the annual average has little impact. Nonetheless, we operationally had to make a choice between summertime and annual averages. We used summertime for our offset correction because there is evidence that skeletal growth of B. elegans and other closely related cold-water coral species is biased towards summer35,46,47 (Supplementary Methods 1.3).

Unlike ΔpCO2, to most accurately reconstruct ΔpH, the process driving this shift in pH should be known. Different biogeochemical processes lead to different paths in pH-DIC space between the δ11B curves representing modern and historic coral data. This choice of path will result in slightly different implied ΔpH values (but does not significantly impact ΔpCO2). For example, if most of the Salish Sea seawater changes captured by δ11B were driven by accumulation of anthropogenic CO2, then the implied pH would be slightly smaller than if seawater chemistry changes were primarily driven by shifts in ecosystem calcification and CaCO3 dissolution (see colored paths in Supplementary Fig. 4). We assume that CO2 invasion is the main driver of the 20th-century change (as explained in Supplementary Discussion 1.1), which constrains the historic estimate of DIC and allows us to calculate an absolute estimate of historic pH. This biogeochemically reasonable assumption also leads to a smaller, more conservative ΔpH estimate than other processes, like shifts in calcification and CaCO3 dissolution. Note again that the sensitivity of ΔpH to the choice of processes is small compared to other sources of uncertainty. The intersections of the CO2 invasion line and historic and modern coral records in Supplementary Fig. 4 imply ΔpH=−0.095 (standard error of the difference between modern and historic = 0.025). The mean DIC is 28 µmol/kg. This estimate is in the same range as estimates of ΔDIC in the Salish Sea from a high-resolution biophysical modeling study48.

Despite the coral-based ΔpH and ΔpH of the open surface ocean over the past century being comparable in magnitude (~−0.1), the mean chemical state of the open ocean surface is vastly different than that at depth in the Salish Sea; therefore, the same amount of atmospheric CO2 change will lead to different changes in pH dependent on the background carbonate chemistry of the system.

The Salish Sea has a higher DIC:TA value than the open ocean surface and thus a lower buffering capacity. To understand the effect of this background state on subsequent changes in carbonate chemistry, we can calculate the predicted ΔpH in our ‘baseline’ scenario, defined as the magnitude of acidification associated with the uptake of atmospheric CO2 over the industrial era (ΔCO2atm = 120 ppm between 1900 and 2020). Feely et al. 201049 Table 1 provides historic and modern estimates for DIC, TA, and pH at depth at Admiralty Inlet, where the majority of our corals were collected. From these variables, we can calculate historic pCO2 and estimate modern pH assuming modern pCO2 = historic pCO2 + 120 µatm (the change in atmospheric CO2 over the 20th century). The predicted ΔpH for this baseline scenario is −0.06, far smaller than the −0.095 change suggested by the coral record. Furthermore, the absolute change in [H+] is 1.5 times larger in the Salish Sea (associated with the baseline scenario yielding a −0.06 pH decline) versus that in the open ocean (associated with −0.1 pH decline), given the logarithmic nature of the pH scale. For these reasons, the ΔpH in the Salish Sea is in fact amplified when compared to the magnitude of acidification that follows the pace of atmospheric change.

Data processing: coral-based estimates of acidification in the CCS
West Coast δ11B data are interpreted in a similar way as our Salish Sea corals, including the application of a −0.10 pH offset. While the summer and annual pH averages are approximately equivalent in the Salish Sea, locations along the West Coast have different climatologies. The West Coast locations experience low pH earlier in the season compared to the Salish Sea (Supplementary Fig. 3). As a result, the annual and summer pH averages along the West Coast are different, whereas they are approximately equivalent in the Salish Sea. Given that different choices lead to smaller or larger offsets between the West Coast model and coral data, different assumptions can affect the extent of overlap between the coral data and the model. However, all but one combination of these various assumptions is consistent with amplified acidification. Furthermore, the one outlier scenario results in historic pCO2 values that are unrealistically high, so we feel confident in excluding this interpretation from our analysis.

For the reasons described previously, the pCO2 of historic corals in the CCS is well constrained by historic δ11B measurements. These reconstructed pCO2 values are independent of our model and can be compared to modern data, modeled or observational, as well as other proxies. The results of our study are primarily based on these independent pCO2 reconstructions.

It is also convenient to estimate past pH from historic δ11B measurements, even if this requires some other constraint on past DIC. We use an average DIC extracted from the ROMS model by calculating a 7-year summertime average of historic DIC in the nearshore CCS over 0–125 m depth (last 7 years of the historic run). The average DIC value is substituted into Eq. 1, the δ11B-DIC correction equation described above. The δ11B correction values and location-averaged δ11B measurements are then substituted into Eq. 2 to obtain DIC-corrected pH values at each coral location.

The pCO2 data and standard error of the mean values described here represent the y-axis values in Fig. 3. The coral-based calculations of historic pH and pCO2 can be found in Supplementary Table 3.

Data processing: physical-biogeochemical ROMS of the CCS
A regional eddy-resolving physical-biogeochemical Regional Ocean Modeling System (ROMS) was used to assess the change in carbonate chemistry along the US West Coast over the 20th century. Two hindcast simulations were analyzed, spanning 1994–2007 in the modern era and 14 years representing the end of 19th-century conditions as in the historic era. The horizontal grid is 322 × 450 cells with a resolution of dx=12 km, dy=12 km, dt=32 min, and dz=42 terrain-following sigma layers with decreasing layer thickness towards the surface. For the purposes of our analyses, the model results are interpolated to 25-m depth increments and saved as monthly averages. While the modern model has been evaluated against observational data and faithfully reproduces the modern CCS mean state (Supplementary Fig. 6), no long-term dataset exists across the CCS of carbonate chemistry parameters in the early 1900s to assess the accuracy of the historical run. Additional details on the model configuration and reproducibility can be found in Renault et al.50 and Deutsch et al.51. The input for the historical run is based on the input for the hindcast run, with long-term trends of temperature and DIC between the two periods removed. The interannual variability of the surface forcing is the same in both runs. Long-term trends in radiation and relative humidity were removed for the historical run.

The model domain was divided into nearshore (<100 km) and offshore (>200 km) regions during analysis to capture variability in biogeochemical patterns between the coastal CCS and the open ocean. All averages of modeled parameters represent 7-year summertime or annual averages in the historic (last 7 years of the historic run) and modern (December 2000–November 2007) simulations. Only the final seven years of the simulations were included in the calculations to remove model biases due to spin-up and deviations from the mean state, such as the 1997–1998 El Niño.

To compare West Coast coral and model data, the coral data are compared to a modeled summer average, since the corals grow with a seasonal bias in the summer (Supplementary Methods 1.3).

Data processing: model estimates of acidification in the CCS
Model predictions for 20th-century changes in pH, DIC, and pCO2 are assessed along the US West Coast (Supplementary Fig. 7). We primarily analyze acidification in terms of pCO2 as opposed to pH, allowing us to directly compare magnitudes of acidification independent of background carbonate chemistry. Model estimates of ΔpCO2 are also obtained from several depth regimes in the nearshore CCS to align with the coral depths of collection. Above 25 m depth, ΔpCO2 from 1890 to 2005 slightly lags the atmospheric rise in CO2 (ΔDIC = DICmodern – DIChistoric) (ΔpCO2 = 75 µatm; ΔpCO2atm = 80 µatm). At 50–60 m, ΔpCO2 in the nearshore CCS is 120 µatm; at 75–125 m depth, ΔpCO2 in the nearshore CCS is 140 µatm. Summertime averages of ΔpCO2 are also evaluated to compare the coral records, which grow with a seasonal bias (Supplementary Methods 1.3). In the upper 25 m of the water column, ΔpCO2 from 1890 to 2005 in the summer months follow the atmospheric rise in CO2 (ΔpCO2atm = 80 µatm). At 50–60 m depth during the summer, ΔpCO2 in the nearshore CCS is 135 µatm. At 75–125 m depth, ΔpCO2 in the nearshore CCS is 150 µatm. The above summertime ΔpCO2 values at 0–25 m, 50–60 m, and 75–125 m are reproduced in Fig. 3 to represent average model predictions of acidification in the nearshore CCS.

Since no historic-modern pairs exist along the outer West Coast, modeled historic pCO2 and measured historic coral pCO2 are both compared to modern modeled pCO2. Both historic and modern model pCO2 averages are calculated over a 7-year period at every coral location from December 1897 to November 1904 and December 2000 to November 2007, respectively. Since the corals are presumed to grow with a seasonal bias during the summer due to optimized feeding and nutrient supply (Supplementary Methods 1.3), the modern model averages include data only from summer. In all but one location, the season of environmental conditions that aligns with optimal growth corresponds with June, July, and August. Our northernmost location (USNM 92621), however, shows a different climatology where optimized nutrient conditions are delayed. This is likely due to the cumulative seasonal respiration, which contributes to acidified and hypoxic conditions in the northern CCS through the upwelling season, where there is longer retention25,34,52. For this location, we select a 3-month window including July, August, and September. The pCO2 averages are calculated over a 3-cell × 3-cell area (36 km × 36 km) centered on the grid cell nearest the coral location.

The model output is interpolated to 25-m depth intervals. Even though most collection depths are within 5 m of a 25-m increment, USNM 92626, USNM 36416, and USNM 92625 are located halfway between depth bins (Supplementary Data 1). In these cases, the model is linearly interpolated between the two adjacent depth bins to account for pCO2 gradients with depth. The historic, coral-based pCO2 data are plotted against this modern, model-based pCO2 data in Fig. 3 to compare model and geochemical estimates of 20th-century acidification.

Data interpretation: quantifying acidification in the CCS attributed to changes in upwelling and remineralization
To probe the dominant driver of 20th-century acidification, we test for shifts in upwelling and biological activity over the past century using our model. Upwelling strength was evaluated by comparing 7-year averages of upwelling velocity in the nearshore CCS (<100 km) at every depth bin in the historic and modern model simulations. A paired t-test reveals a statistically significant decline in upwelling velocity of 2% in the upper 200 m.

To capture the integrated impact of shifting upwelling patterns and remineralization rates on carbonate chemistry, we calculate the change in apparent oxygen utilization (AOU) over the 20th century. To determine changes in remineralization, we calculate DIC attributed to respiration inferred by AOU and the stoichiometric Hedges ratio in both the historic and modern model simulations53. For AOU calculations, O2 saturation values are calculated at every grid cell in the nearshore CCS for both the historic and modern eras, informed by 7-year averages of temperature and salinity for the given grid cell54. Model O2 is subtracted from saturated O2 to give AOU, or O2remineralization, the oxygen consumed during the transformation of organic matter to inorganic carbon. To obtain DIC produced via remineralization, the AOU was multiplied by the Hedges53 stoichiometric relationship C/O2 = 106/152.5. DIC production attributed to respiration was compared in the historic and modern eras to determine 20th-century changes in remineralization. Supplementary Fig. 9 shows the fraction of ΔDIC that can be explained by 20th-century changes in remineralization (ΔDICremineralization/ΔDIC), which is small relative to other sources of change. Thus, neither shifts in upwelling strength nor changes in remineralization can explain the dominant driver of 20th-century acidification in the CCS.

Data interpretation: quantifying acidification in the CCS attributed to anthropogenic carbon
Anthropogenic carbon is transported to the CCS along isopycnals that initially outcrop in the open ocean. These water masses subduct at the outcrop regions where the water is in exchange with CO2 in the overlying atmosphere. To estimate the change in carbonate chemistry attributed to anthropogenic carbon that enters the ocean at outcrop regions, we calculate the ΔDICpreformed expected from just an increase in atmospheric pCO2:

ΔDICpreformed = DICpreformed,modern − DICpreformed,historic (3)

We assume for this simplified test that the increase in atmospheric pCO2 between the historic and modern eras translates into an equal change in sea surface pCO2. This assumption does not necessarily imply equilibration, but it does make the simplifying assumption of a constant air-sea offset for the outcrop of a particular isopycnal with time. At each grid cell in the CCS, surface, preformed DIC at the outcropping region was calculated using (1) atmospheric CO2 and (2) a 7-year average of the grid cell TA. Note that the difference in preformed DIC between historic and modern is only weakly sensitive to the alkalinity of the preformed water, because contours of constant pCO2 are roughly parallel over the relevant range of carbonate system parameters. Thus, our results are robust to even large uncertainties in mean alkalinity or alkalinity changes.

Water mass age affects our calculations of preformed DIC because this age determines the date when the water mass was most recently in exchange with the atmospheric CO2, which has changed rapidly in the modern era. We assume a typical age structure for the CCS where deeper water masses are older. Our analysis was conducted assuming ages of 0, 13, and 25 years at 0–50 m, 75–125 m, and 150–200 m, respectively, to reflect varying time since last ventilation. In the modern model (2000–2007), these ages correspond with atmospheric CO2 concentrations of 376, 360, and 339 µatm for ~2005, 1995, and 1980, respectively (Switzerland Institute for Atmospheric and Climate Science, Annual CO2 Data). Given the rapid rise of atmospheric CO2 since the 1970s, accounting for water mass age is an important consideration when analyzing acidification patterns in the CCS. In the historic model (end of 19th century), atmospheric CO2 was relatively constant over the prior 25 years, so water mass age makes little difference in terms of anthropogenic carbon accumulation (CO2atm = 296 µatm).

The difference between modern and historic preformed DIC values represents the estimated ΔDIC attributed to anthropogenic carbon (ΔDICpreformed, Eq. 3). The ratio of estimated, preformed ΔDIC to modeled ΔDIC is calculated at every grid cell to determine how much modeled 20th-century changes can be explained by uptake of anthropogenic CO2. Supplementary Fig. 10 shows the percent that uptake of anthropogenic CO2 can explain modeled ΔDIC at 0–50 m, 75–125 m, and 150–200 m, depth, assuming structured water mass age. Estimates of preformed ΔDIC derived from equilibration of atmospheric CO2 at outcropping regions and accompanying thermodynamic buffering effects can explain modeled ΔDIC within 15% relative error. The remaining residual leaves room for second-order effects such as changes in upwelling strength and biological activity, independently estimated based on AOU calculations and model-based upwelling parameters, described above.

Modeled and estimated acidification attributed to anthropogenic carbon were also compared in terms of pCO2 and pH. Estimates of modern DIC assuming atmospheric CO2 invasion and thermodynamic buffering effects are obtained by adding the preformed ΔDIC from Eq. 3 to a 7-year modeled average of historic DIC at each grid cell (Eq. 4). The 7-year average of modeled modern TA and the estimate of modern DIC from Eq. 4 inform estimates of pCO2 and pH.

DICestimate,modern = DICmodel,historic + ΔDICpreformed (4)

Peer review rounds
[{"round": 1, "reviewer_comments": {"reviewer_2": "I commend the authors for combining paleo data with a modelling approach, which is a fresh and valuable contribution on a\nvery relevant topic. However, I am concerned about the use and presentation of the historical paleo data. While the\nmanuscript aims to compare present-day and historical paleorecords, the historical data seem relegated to the Extended\nData and Supplementary Information, which diminishes their significance. The historical records are extensively discussed\nin the main text, yet the figures and some details are buried in the Extended Data and Supplementary Information. The\nSupplement should complement the main text, not serve as the primary presentation of critical results. This approach makes\nit difficult to fully appreciate the historical datasets, and the study appears overly reliant on the model data as a result. Why\nnot show some of the historical data in figures 2 or 3?\nThe authors emphasize CO₂ as the focal point of their discussion, given its comparative utility across locations. However,\nCO₂ estimates depend on assumptions about DIC, which introduce additional layers of uncertainty. Moreover, the\ntemperature effect on the k value is not incorporated into the calculation of pH from δ¹¹B. Addressing these uncertainties\nexplicitly would strengthen the study.\nWhile the combination of paleo and modelling approaches holds promise, the manuscript would benefit from a clearer and\nmore prominent presentation of the historical datasets. Improving transparency regarding uncertainties, sampling strategies,\nand data handling would greatly enhance the robustness of the study.\nSpecific Comments:\n• Figure 3, panel e: The description of the presented data should clarify that it represents modelled data. Why are the\nhistorical coral data not included in this figure?\n• Line 15: Consider revising “the leading edge” to “a leading edge,” depending on the context.\n• Line 107: What about intraspecies variability, such as vital effects? This point needs clarification.\n• Line 142: Specify explicitly that this refers to data from Gagnon et al. (2021).\n• Line 609: The sampling strategy requires further detail. This concern was raised previously by reviewers, yet the revisions\nstill lack sufficient information regarding how the corals were sampled. E.g., which skeletal elements were sampled,\ndistance, etc.\nAdditionally, potential offsets in the data could result from treatment effects (e.g., preferential dissolution of skeletal elements\nlike the centres of calcification) or sampling strategies that selectively represent certain skeletal components.\nIn this sense, is there any information on how the historical corals were treated post-collection, such as cleaning or\npreservation procedures?\nFurthermore, as indicated by the authors critical information is lacking for some historical samples, particularly sample 7863.\nWhy was dating not performed on this sample? Providing this detail could help address gaps in the dataset.", "reviewer_3": "Review: A Century of Change in the California Current: Upwelling System Amplifies Acidification\nThe current study investigates the speed of ocean acidification (OA) in the California Current System (CSS), a system where\nlocal waters are naturally acidified due to the upwelling of CO2 enriched deep water. To estimate the pace of OA in the CSS\ncompared to the global open ocean average, the authors rely in the first instance on the comparison of the δ11B signal in the\nskeletons of deep-water coral (Balanophyllia elegans) which were collected recently and at the beginning of the industrial\nera. To identify which processes drive OA in the CSS and the Salish Sea the authors then use a regional ocean modelling\nsystem (ROMS) and a box model (Salish Sea). The authors find that the mean skeletal δ11B signal of historic coral is\nsignificantly higher than that of modern coral which suggests a change over the last 100 years of 172 ± 41 µatm regarding\npCO2 and -0.095 pH respectively. However, this change is not uniform, and OA appears to be especially\namplified at depths below 50m. The two models generally support the geochemical record and\nsuggest that the main drivers for the acceleration of OA in the CSS are the increase in atmospheric\nCO2 as well as a thermodynamic buffering effect. The study send to us for review has gone through\nan extensive peer review process already. We felt that the comments from the previous reviewers\nhave been adequately addressed and that the study is overall well executed and the results credible.\nThus, we have very little to criticize. Nonetheless, there are a few things that require further\nclarification in our opinion. Thus, we recommend the paper to undergo minor revisions before\npublication can considered. Detailed comments below.\nComments:\nThe collection of the skeletal material for the δ11B requires some further clarification. The authors write that 3 to 9 mg of\nmaterial was collected from along the primary growth axis. So, does the collected/analyzed material represent the average\nover the whole growth period? How fast do these corals grow and how old to they get? The age of the historic coral at the\ntime of collection is unlikely to affect the study outcome as pH values were, assumedly, relatively stable. However, if\nthe modern coral are 100 years old the presented data would represent the average conditions over the whole period. Thus, if\nthe authors would have considered only the most recently deposited material, then the pace of OA in the system may have\nbeen even faster.\nRelated to this, if the analyzed material indeed represents an average then this may, however, impact the depth-acidification\npatterns observed. If the populations in the different depth strata have a different age structure, then you would over or\nunderestimate the pace of OA. For example, if the samples from the 75m stratum are the youngest then that would indeed\nsuggest a faster pace of OA in that layer compared with the rest. Thus, I think it is important to provide some estimates of\ntheir respective age at these different depths.\nL350 in the Supplementary Material: A change in river water discharge was discarded by the authors as the most likely\ncause for causing the observed patterns in acidification. The authors make this assumption on the data from the from the\nSkagit River Gauge using data from 1940–2020. Older data is then extrapolated. However, three major dams (Ross,\nDiablo and Gorge) of the Skagit River were completed or nearly completed before that (1924, 1936, and 1940). Thus, the\nextrapolation likely underestimates any changes in river discharge since they only incorporate data after major dams have\nbeen built. This requires some more research and justification from the authors.\nExtended Data Figure 3: Looking at the observational data. It seems that they fall in between the mixing/upwelling line and\nCO2 invasion/photosynthesis line suggesting an influence of both processes. Can the authors clarify how this would affect\nthe calculation of their pH and pCO2 trends over time and why this can be excluded?\nSupplementary material L406-409: What is the reason for not having considered the input from the Skagit River? In the\nprevious paragraphs the authors have highlighted the contribution of its water to the basin “variation in Salish Sea carbonate\nchemistry is strongly influenced by water mass mixing”, “The Skagit River represents the largest freshwater input to Puget\nSound” and “Furthermore, normalizing the TA and DIC for salinity causes the data to collapse and a majority of the seasonal\nvariability is removed”.\nFor their simulations it seems that the authors have selected to present their data on the seawater scale while the\ngeochemical data return pH on the total scale. Since the authors are interested in comparing respective differences the\noutcome for the study is the same. Also, the choice of the authors for focusing on changes in pCO2 also avoids some of the\npotential pitfalls there. However, could the authors confirm that there are not any differences introduced by selecting two\ndifferent pH scales? I was also wondering whether it would not be better to also or solely present the modelled data on the\ntotal scale to make them match with the geochemical records and the discrete water samples. I gathered that these mostly\nreport pH on the total scale.\nMinor comments:\nFig1b: Isn’t the CSS also a source of CO2(atm)? The authors could consider adding an arrow going back to the atmosphere.\nL241: Likely that we missed it but how was upwelling velocity calculated and what is the underlying data for it?\nL643: Regarding the t-test for the coral samples and all other test performed. How were the test assumptions (e.g., normality)\nassessed?\nFigure 2: It appears that the error bars are in some cases taken from the population mean. I am\nunfamiliar with this approach and wonder how reliable these are? In any case, it is unclear to us with population(s) are the respective values taken from? I think the authors don’t loose much\nremoving the bars for those samples where this was done (n=1) if they decide to keep them than it should be clear where they come from.\nL203: I find the word reproduce is a bit odd here. We’d argue that the coral record represents the more solid data,\neven though it is only proxy data, and thus the model is the one that reproduces patterns.\nL709: I find the references used here slightly misleading. It sounds like they support the statement regarding elevated growth\nof B. elegans in summer but actually both references only make statements with regard to another cold-water coral (D.\ndianthus). The authors themselves write this out a bit more clearly in the Supplementary Material. I agree that some\nsimilarities can be inferred here but some caution must be taken with making these statements as we are dealing with a\ndifferent species here and likely also different systems. Also, do the authors have more evidence to offer that summer\nconditions in the CSS could indeed facilitate growth of B. elegans in summer?\nExtended data:\nExtended Data Figures 7 & 8: Suggest using a different scale of colours to better differentiate the area of interest (especially\nwhen values are close to 1) from the background.\nSupplementary material\nL43-45: A reference should be added to support this concept. I suggest Chan 2017 (doi: https://doi.org/10.1038/s41598-017-\n02777-y) and/or Reum 2015 (doi: https://doi.org/10.1093/icesjms/fsu231).\nL66-73: Some of these statements would benefit from a reference to back them up.\nFigure S1.1 & S1.2: The resolution seems very low. Also, check title and axis labels for S1.2.\nL204: Table description above the table.\nL220: “0” missing for -.101 offset.\nL344: The use of “Although” makes the sentence in contraposition with what has been said before, while it is not.\nL346: Check 2nd citation of Kroeker et al. 2013. The citation got his own sentence there.\nLine 487/Figure S3.2: See comment reading Figure 2 above.\nLine 517: I think here a brief description of the methodology could be useful instead of only referring the reader to another\npaper.", "reviewer_4": "I co-reviewed this manuscript with one of the reviewers who provided the listed reports. This is part of the Nature\nCommunications initiative to facilitate training in peer review and to provide appropriate recognition for Early Career\nResearchers who co-review manuscripts."}, "author_response": "Responses to Reviewer Comments\n‘A Century of Change in the California Current: Upwelling System Amplifies Acidification’\nWe thank all referees for their thorough assessment of our work, careful reading of the manuscript,\nand numerous insightful comments and suggestions. These thoughtful reviews provided an\nopportunity to clarify important points and details concerning the interpretation and assumptions\nmade in our analyses. Below please find a point-by-point response to all comments, along with a\nrevised manuscript with tracked changes that reflect the constructive feedback provided in review.\nREVIEWER COMMENTS\nReviewer #3 (Remarks to the Author):\n“The current study investigates the speed of ocean acidification (OA) in the California Current\nSystem (CSS), a system where local waters are naturally acidified due to the upwelling of CO2\nenriched deep water. To estimate the pace of OA in the CSS compared to the global open ocean\naverage, the authors rely in the first instance on the comparison of the δ11B signal in the skeletons\nof deep-water coral (Balanophyllia elegans) which were collected recently and at the beginning of\nthe industrial era. To identify which processes drive OA in the CSS and the Salish Sea the authors\nthen use a regional ocean modelling system (ROMS) and a box model (Salish Sea). The authors\nfind that the mean skeletal δ11B signal of historic coral is significantly higher than that of modern\ncoral which suggests a change over the last 100 years of 172 ± 41 µatm regarding pCO2 and -\n0.095 pH respectively. However, this change is not uniform, and OA appears to be especially\namplified at depths below 50m. The two models generally support the geochemical record and\nsuggest that the main drivers for the acceleration of OA in the CSS are the increase in atmospheric\nCO2 as well as a thermodynamic buffering effect. The study send to us for review has gone through\nan extensive peer review process already. We felt that the comments from the previous reviewers\nhave been adequately addressed and that the study is overall well executed and the results credible.\nThus, we have very little to criticize. Nonetheless, there are a few things that require further\nclarification in our opinion. Thus, we recommend the paper to undergo minor revisions before\npublication can considered. Detailed comments below.”\nComments:\n“The collection of the skeletal material for the δ11B requires some further clarification. The\nauthors write that 3 to 9 mg of material was collected from along the primary growth axis. So, does\nthe collected/analyzed material represent the average over the whole growth period? How fast do\nthese corals grow and how old to they get? The age of the historic coral at the time of collection is\nunlikely to affect the study outcome as pH values were, assumedly, relatively stable. However, if\nthe modern coral are 100 years old the presented data would represent the average conditions over\nthe whole period. Thus, if the authors would have considered only the most recently deposited\nmaterial, then the pace of OA in the system may have been even faster.”\n• We thank Reviewers #3 and #4 for their valuable insights and helpful suggestions. This\ncomment provided the opportunity to clarify an important detail previously missing from\nthe Methods section discussing boron isotope analyses and interpretation. These\nclarifications have been added to our Methods section (lines 419-431 and 434-453), and\nwe thank the reviewers for raising this point.\n• The reviewers are correct that the collected/analyzed material represents an average over\nthe entire growth period, however this is relatively short: it has been estimated that the\naverage life span for B. elegans in the California Current is 6.5 to 11 years (Fadlallah 1983).\nAs noted, the age of the historic coral at the time of collection is unlikely to affect the study\noutcome, as pH values were assumed to be relatively stable. The age of the modern corals\nis also unlikely to impact the modern pH values, as they represent conditions over a narrow\ntime window (5-10 years). Given that the modern corals were collected in 2020, they reflect\nconditions from approximately 2010 to 2020. Any uncertainty in the exact age and\ntherefore assumed pace of acidification over this period is within the measurement error of\nthe corals.\n“Related to this, if the analyzed material indeed represents an average then this may, however,\nimpact the depth-acidification patterns observed. If the populations in the different depth strata\nhave a different age structure, then you would over or underestimate the pace of OA. For example,\nif the samples from the 75m stratum are the youngest then that would indeed suggest a faster pace\nof OA in that layer compared with the rest. Thus, I think it is important to provide some estimates\nof their respective age at these different depths.”\n• We thank the reviewers for carefully considering how these factors may influence the\ninterpretation of coral data. We have added several sentences to the Methods section\n(Sample Collection, lines 419-431) to discuss coral ages and highlight the narrow time\nframe during which the historic corals from the CCS were collected.\n• While we have not found any evidence to suggest that populations at different depth strata\nhave different age structure, this effect is unlikely to impact our study results given that\neach coral represents conditions over such a narrow time window. Additionally, all of the\nhistoric corals in the CCS were collected within 1.5 years of each other (September 1888\nto March 1890). The natural pCO gradient with depth is also much larger than differences\n2\nin the pace of OA over a 5-10 year time period.\n“L350 in the Supplementary Material: A change in river water discharge was discarded by the\nauthors as the most likely cause for causing the observed patterns in acidification. The authors\nmake this assumption on the data from the Skagit River Gauge using data from 1940–2020. Older\ndata is then extrapolated. However, three major dams (Ross, Diablo and Gorge) of the Skagit River\nwere completed or nearly completed before that (1924, 1936, and 1940). Thus, the extrapolation\nlikely underestimates any changes in river discharge since they only incorporate data after major\ndams have been built. This requires some more research and justification from the authors.”\n• The reviewers raise an interesting concern regarding our assumptions about major dams on\nthe Skagit River. We acknowledge that our extrapolation likely underestimates changes in\nriver discharge, as the river gauge was put in place after major dam construction. To assess\nthe implications for our acidification estimates and interpretation, we conducted additional\nresearch. A summary of this analysis is now included in Supplementary Discussion 1.1\n(lines 428-456), with details provided below.\n• First, we identified another USGS River Gauge (12194000) on the Skagit River that\nextends further back in time to 1925. We found that Gorge Dam, Diablo Dam, and Ross\nDam were completed in 1924, 1931, and 1940, respectively (Skagit County Basin\nOverview Report). This river discharge record includes data before the completion of the\nDiablo and Ross dams, but after the Gorge Dam was built. Among these, only Ross Dam\nis a storage dam, meaning it had the potential to significantly reduce natural spring river\nflows from snowmelt (Pacific International Engineering, 2008). The impact of the Ross\nDam, which most likely influenced acidification the most as a large storage dam, is\ncaptured in the new river gauge data.\n• We applied the same analysis as described in Supplementary Discussion 1.1 to evaluate\nwhether a shift in mixing could have driven 20th century acidification. A best-fit linear\nregression was applied to USGS River Gauge (12194000), and we found that river\ndischarge actually increased by ~5% between 1925–2020. However, this period includes\nthe Dust Bowl, which caused prolonged droughts and several consecutive low-\nprecipitation years between 1928 and 1942 (Washington State Governor’s Report). If we\nassume that the pre-drought years better represent historical conditions (after Gorge Dam\nwas built), we estimate that river discharge declined by ~6%.\n• We also consulted with the Army Corps of Engineers, who manage the Skagit River dams,\nbut they unfortunately did not have records of river flow before Gorge Dam was built in\n1924. However, given that Gorge Dam was not a storage dam, this absence of data is\nunlikely to affect our conclusions.\n• Thus, while dam construction likely influenced carbonate chemistry in the Admiralty Inlet\narea, the corals conservatively suggest that river discharge would have had to decline by\nover 20% to explain the observed acidification. Although dam construction likely\ninfluenced carbonate chemistry to some extent in the Salish Sea, changes in river discharge\nstill cannot account for the main driver of acidification.\n“Extended Data Figure 3: Looking at the observational data. It seems that they fall in between the\nmixing/upwelling line and CO2 invasion/photosynthesis line suggesting an influence of both\nprocesses. Can the authors clarify how this would affect the calculation of their pH and pCO2\ntrends over time and why this can be excluded?”\n• Changes in seawater chemistry over the past century are bounded by historic (green line)\nand modern (gray line) coral data in what is now Supplementary Fig. 4. Since the contour\nlines of constant pCO (black dashed lines) and the coral-derived bounds on pCO are\n2 2\nroughly parallel, the coral data constrain pCO tightly without additional process-based\n2\ninformation. However, to better understand the dominant mechanism of acidification, we\nconducted additional analyses and process studies to explore potential drivers.\n• The observational data in Supplementary Fig. 4 represent the seasonality of carbonate\nchemistry at the Washington Ocean Acidification Center (WOAC) station 21. The reviewer\ncorrectly notes that the data fall between the mixing/upwelling line and CO\n2\ninvasion/photosynthesis lines, suggesting that all three processes influence seasonal\ncarbonate chemistry in the Salish Sea. However, the observed pH and pCO changes\n2\ndepend on assumptions about how these processes changed over the past century. To\nevaluate the dominant driver of 20th century acidification, Supplementary Discussion 1.1\npresents process-based arguments for each mechanism shown in Supplementary Fig. 4. We\nfind it is unlikely that changes in calcification, photosynthesis, or mixing ratios alone could\nexplain the observed acidification.\n• As a sensitivity test, we hypothesized that acidification over the past century was driven\nby a shift in the seasonality of carbonate chemistry in the Salish Sea. To estimate changes\nin pH and pCO , we fit a best-fit line through the observational data (which accounts for\n2\nall processes described above), and calculated its intersections with the historic and modern\ncoral data. Under this assumption, ΔpCO = 169 uatm, which is well within the uncertainty\n2\nrange of our estimate of ΔpCO = 172 uatm under the assumption of CO invasion. In short,\n2 2\nregardless of the assumed dominant process driving acidification, the overall magnitude of\nacidification is well constrained because δ¹¹B provides such a strong bound.\n“Supplementary material L406-409: What is the reason for not having considered the input from\nthe Skagit River? In the previous paragraphs the authors have highlighted the contribution of its\nwater to the basin “variation in Salish Sea carbonate chemistry is strongly influenced by water\nmass mixing”, “The Skagit River represents the largest freshwater input to Puget Sound” and\n“Furthermore, normalizing the TA and DIC for salinity causes the data to collapse and a majority\nof the seasonal variability is removed”.”\n• The purpose of this box model was to provide a simple estimate of acidification in the\nSalish Sea, independent of the coral records. To achieve this, we included only the\ndominant mechanism likely to drive acidification over the 20th century, as identified\nthrough the process-based arguments in Supplementary Discussion 1.1. Based on these\narguments, we find that CO invasion was the most likely primary driver.\n2\n• To evaluate acidification under this mechanism, we created a box model that estimates\nacidification solely driven by CO invasion. Therefore, the model incorporates two key\n2\nprocesses: estuarine circulation of upwelled waters from the CCS, which contain imprints\nof atmospheric CO from when they were last at the surface, and air-sea gas exchange in\n2\nthe Salish Sea estuary.\n• While the Skagit River plays an important role in the seasonality of carbonate chemistry in\nthe Salish Sea, this box model focuses on long-term mean state changes over the 20th\ncentury. As discussed in Supplementary Discussion 1.1, we find that changes in river flow\nover the past century were unlikely to be the dominant driver of acidification.\n• The close alignment between the coral-based and box model-based estimates of ΔpCO\n2\nsuggest that anthropogenic carbon, modulated by estuarine circulation and air-sea gas\nexchange, can account for the primary driver of 20th century acidification.\n“For their simulations it seems that the authors have selected to present their data on the seawater\nscale while the geochemical data return pH on the total scale. Since the authors are interested in\ncomparing respective differences the outcome for the study is the same. Also, the choice of the\nauthors for focusing on changes in pCO2 also avoids some of the potential pitfalls there. However,\ncould the authors confirm that there are not any differences introduced by selecting two different\npH scales? I was also wondering whether it would not be better to also or solely present the\nmodelled data on the total scale to make them match with the geochemical records and the discrete\nwater samples. I gathered that these mostly report pH on the total scale.”\n• We thank the reviewers for highlighting this point regarding pH scales and the presentation\nof both modeled and geochemical data. The reviewers are correct that our focus on pCO\n2\nand respective differences between historic and modern eras avoids complications\nassociated with using two pH scales. However, to maintain consistency, we updated what\nare now Figures 4a and 4c to show modeled data on the total pH scale. Changes to the plot\nare minimal; the difference between the total and seawater scales is typically on the order\nof 0.01 pH units, whereas the color bar in Figure 4a spans 0.3 units.\nMinor Comments:\n“Fig1b: Isn’t the CSS also a source of CO (atm)? The authors could consider adding an arrow\n2\ngoing back to the atmosphere.”\n• The reviewers are correct that the CCS also acts as a source of CO (atm) in some regions\n2\nand seasons. We did actually consider adding an arrow near the upwelling region to show\noutgassing, but we decided to simplify the figure to emphasize processes relevant to the\namplification effect.\n“L241: Likely that we missed it but how was upwelling velocity calculated and what is the\nunderlying data for it?”\n• The upwelling velocities are extracted from the model output; details regarding the\ncomputation be found in Shchepetkin and McWilliams, 2008 (page 150).\n“L643: Regarding the t-test for the coral samples and all other test performed. How were the test\nassumptions (e.g., normality) assessed?”\n• Normality was evaluated for all statistical assessments using the Shapiro-Wilk test in\npython using the sci-kit learn package. The historic dataset from the West Coast and\nhistoric and modern datasets from the Salish Sea all appeared to be normally distributed.\n“Figure 2: It appears that the error bars are in some cases taken from the population mean. I am\nunfamiliar with this approach and wonder how reliable these are? In any case, it is unclear to us\nwith population(s) are the respective values taken from? I think the authors don’t lose much\nremoving the bars for those samples where this was done (n=1) if they decide to keep them than it\nshould be clear where they come from.”\n• At locations where there was only one coral, we used the population standard deviation to\nrepresent the standard error of the mean. The population standard deviation was inferred\nby calculating the average of standard deviations at locations with 8+ samples, excluding\nUSNM 7863 located in a highly variable tidepool environment. This method is described\nunder Methods, ‘Coral-Based Estimates of Acidification in the CCS’; we added more detail\nto clarify where this value is derived. Brief information is included in the Figure 2 (now\nFigure 3) caption, but we also added a reference to the Methods section to provide more\ndetail if the reader is interested (line 788-789).\n• This is a conservative approach meant to indicate that there is also error associated with\nlocations that have only one coral. The alternative of removing error bars for locations with\nonly one coral could lead the reader to think that these locations are better known than they\nare. However, if the reviewers prefer we remove the error bars in Figure 3, we are open to\ndoing so.\n“L203: I find the word reproduce is a bit odd here. We’d argue that the coral record represents the\nmore solid data, even though it is only proxy data, and thus the model is the one that reproduces\npatterns.”\n• We thank the reviewers for pointing this out. We agree that the coral record represents\nmore solid data and changed the phrasing of this sentence to reflect this perspective.\n“L709: I find the references used here slightly misleading. It sounds like they support the statement\nregarding elevated growth of B. elegans in summer but actually both references only make\nstatements with regard to another cold-water coral (D. dianthus). The authors themselves write this\nout a bit more clearly in the Supplementary Material. I agree that some similarities can be inferred\nhere but some caution must be taken with making these statements as we are dealing with a\ndifferent species here and likely also different systems. Also, do the authors have more evidence\nto offer that summer conditions in the CSS could indeed facilitate growth of B. elegans in\nsummer?”\n• Thank you for pointing out this missing information from the Methods section. We agree\nthis is important information to include in the Methods for transparency, regardless of the\ndetail included in the Supplementary Material. We added a statement to the Methods\nsection (lines 663-665) to specify that these references describe growth patterns from a\ndifferent but closely-related cold-water coral species.\n• Further research provided additional evidence that summer conditions in the CCS could\nfacilitate growth of B. elegans. Fadlallah 1983 discovered that food availability, as a result\nof upwelling, could promote growth and larval settlement. We included this additional\nreference in the Methods (lines 663-665) and Supplementary Methods 1.3 (lines 232-234)\nsections.\nExtended Data:\n“Extended Data Figures 7 & 8: Suggest using a different scale of colours to better differentiate the\narea of interest (especially when values are close to 1) from the background.”\n• We agree that a different color bar would better differentiate the important areas in these\nfigures (now Supplementary Fig. 9 and 10). We updated these figures with a new color bar.\nSupplementary Material:\n**We reordered the Supplementary Information sections and divided the text into Supplementary\nMethods and Discussion sections. We include updated line numbers for the relevant revisions\nbelow.\n“L43-45: A reference should be added to support this concept. I suggest Chan 2017\n(doi: https://doi.org/10.1038/s41598-017-02777-y) and/or Reum 2015\n(doi: https://doi.org/10.1093/icesjms/fsu231).\n• We agree that this statement is best supported by references to other studies. Thank you for\nproviding these two articles – we included these references in lines 826-827.\n“L66-73: Some of these statements would benefit from a reference to back them up.”\n• We agree that these statements are best supported by references to back them up. We\nincluded additional references in lines 847-855.\n“Figure S1.1 & S1.2: The resolution seems very low. Also, check title and axis labels for S1.2.”\n• Thank you for pointing out these figure errors. We updated (now) Supplementary Fig. 14\nwith higher resolution and corrected the labels.\n“L204: Table description above the table.”\n• Thank you for catching this error. We moved the caption for Table S2.1 above the table.\n“L220: “0” missing for -.101 offset.”\n• Thank you for catching this error. We added a ‘0’ preceding the offset value.\n“L344: The use of “Although” makes the sentence in contraposition with what has been said\nbefore, while it is not.”\n• We can see how this statement may cause confusion, so we clarified this explanation in the\nSupplementary Discussion 1.1 (lines 393-401).\n“L346: Check 2nd citation of Kroeker et al. 2013. The citation got his own sentence there.”\n• Another great catch – thank you! We deleted the 2nd citation of Kroeker et al. 2013 in line\n346.\n“Line 487/Figure S3.2: See comment reading Figure 2 above.”\n• Thank you for noting the error bars in Figure S3.2 as well – response is as for what was\npreviously Figure 2, now Figure 3.\n“Line 517: I think here a brief description of the methodology could be useful instead of only\nreferring the reader to another paper.”\n• I believe the reviewers here are referring to the Osborne et al. 2020 study, which\nreconstructed carbonate chemistry in the California Current using fossil foraminifera tests.\nThe paragraphs between lines 690-707 provide a brief overview of the methodology used\nin Osborne et al. 2020 and describe how we utilized the data published in that study to\ncompare to our coral record. We are unclear on the methodological scope that the reviewers\nare referring to, but we are happy to include additional detail with more direction.\nReviewer #4 (Remarks to the Author):\n“I co-reviewed this manuscript with one of the reviewers who provided the listed reports. This is\npart of the Nature Communications initiative to facilitate training in peer review and to provide\nappropriate recognition for Early Career Researchers who co-review manuscripts.”\n• We thank Reviewer #3 and #4 for their careful reading of the manuscript, and numerous\ninsightful comments and suggestions.\nReviewer #2 (Remarks to the Author):\n“I commend the authors for combining paleo data with a modelling approach, which is a fresh and\nvaluable contribution on a very relevant topic. However, I am concerned about the use and\npresentation of the historical paleo data. While the manuscript aims to compare present-day and\nhistorical paleorecords, the historical data seem relegated to the Extended Data and Supplementary\nInformation, which diminishes their significance. The historical records are extensively discussed\nin the main text, yet the figures and some details are buried in the Extended Data and\nSupplementary Information. The Supplement should complement the main text, not serve as the\nprimary presentation of critical results. This approach makes it difficult to fully appreciate the\nhistorical datasets, and the study appears overly reliant on the model data as a result. Why not\nshow some of the historical data in figures 2 or 3?”\n• We thank the reviewer for their thoughtful feedback and appreciation of our approach to\nintegrate paleo data with modeling. We understand the concern regarding the placement of\nhistorical data and appreciate the opportunity for revision. Based on reviewer feedback, we\nembraced the core data of the study and moved what was previously Extended Data Figure\n2 of Salish Sea paleo proxy data to the main text (now Figure 2). This figure shows the\nprimary geochemical signal and that there is a significant difference between historic and\nmodern corals collected from the same locations. Our efforts to better highlight\ngeochemical data in the manuscript are discussed in more detail below.\n• Salish Sea data:\no The historic and modern coral records from the Salish Sea are now displayed in the\nmain text as Figure 2. This geochemical data was distilled down to a single delta\nvalue (as discussed in Supplementary Methods 1.1) that captures the magnitude of\nacidification over the 20th century in terms of pCO and pH. The significance of\n2\nthis value is thoroughly discussed in the main text, where we compare these\nchanges to expectations if acidification had followed atmospheric trends. The\nobserved changes in pCO (+172 µatm) and pH (-0.095) from the coral records\n2\nindicate that the Salish Sea experienced amplified acidification over the 20th\ncentury. This was the key takeaway from the Salish Sea geochemical data, and the\nadded representation of this geochemical data in the main text emphasizes their\nimportance to this study.\n• West Coast data:\no The historical West Coast coral data are presented in what is now Figure 3. The\nvalues on the y-axis for each data point represent historic pCO averaged at each\n2\ncoral location. The n= # values next to each data point represent the number of\ncorals that were averaged together at that location. The magnitude of acidification\nover the 20th century produced in the model is represented by the dashed lines to\nreflect different depth bins. This figure attempts to synthesize both geochemical\nand modeled data and emphasize how the magnitude of amplified acidification\nincreases with depth in the CCS.\no We chose to exclude the geochemical data from the West Coast (in what is now\nmain text, Figure 2) because there is only historic data. Therefore, we thought our\ntarget audience would not find a direct, geochemical representation as intuitive\nwithout a comparison to modern data for context. The individual and location-\naveraged skeletal data from the West Coast can be found in Supplementary Fig. 2.\no Figure 3e (now Figure 4e) shows modeled averages of seawater pCO across the\nbecause the corals were collected across a broad geographic and depth range with\nhigh variability in background seawater chemistry, making them unsuitable for\nbasin-wide and depth-bin averaging. The variability across sites and depths can be\nseen by the spread in historic pCO values along the y axis in Figure 3. Therefore,\n2\nthe coral data would not ‘bin’ adequately into the regional and depth bins of Figure\n4.\n• Supplementary figures:\no Supplementary Fig. 2 presents skeletal δ11B data from individual corals and\nlocation averages from the Salish Sea and West Coast. Supplementary Fig. 2b is\nnow reproduced in the main text to more prominently display the historic and\nmodern geochemical data from the Salish Sea.\n• We hope the above explanation clarifies our rationale for the balance between content in\nthe main text and Supplementary Information. We are open to relocating additional content\nif the reviewer has specific suggestions.\n“The authors emphasize CO₂ as the focal point of their discussion, given its comparative utility\nacross locations. However, CO₂ estimates depend on assumptions about DIC, which introduce\nadditional layers of uncertainty. … Addressing these uncertainties explicitly would strengthen the\nstudy.”\n• We thank the reviewers for pointing this out and appreciate the opportunity to clarify this\nimportant methodological detail. The main text (lines 129-136) now notes that the coral\nrecords provide a tight constraint on pCO and references Supplementary Fig. 4. This\n2\nrevision includes an additional reference in the main text (line 136) to Methods (Coral-\nBased Estimates of pCO ), where these assumptions and uncertainties are discussed. We\n2\nalso explicitly mention the robustness of pCO estimates to ‘changes in DIC’ in line 135 to\n2\nimprove transparency. We also add a sentence to the Methods to explicitly state that the\neffect of DIC falls within measurement error of the corals (lines 562-564) and is not\nnecessary to constrain our estimates of acidification (lines 568-571).\n• One of the main points of the study is that δ11B provides a strong constraint on pCO\n2\nregardless of the DIC value. To show this, we plot how a specific d11B value would be\nrepresented in pH vs DIC space in Supplementary Fig. 4. Historic and modern skeletal δ11B\nmeasurement averages in the Salish Sea are indicated by solid lines. We found that δ11B\nprovides a strong constraint on pCO regardless of the DIC value. Across a large range of\nrepresenting specific seawater pCO values. This indicates that the corals provide a robust\n2\nestimate of pCO changes over the past century, even if DIC is not well known. While it is\n2\nuseful to have a rough idea of DIC for the general region of the ocean where the coral grew\nto best plot the right area of pH vs DIC space, this rough regional DIC does not need to be\nwell known. The uncertainty in the selected DIC value to operationally calculate ΔpCO\n2\nis\nwell within measurement error and averaging error of the corals across locations.\n“Moreover, the temperature effect on the k value is not incorporated into the calculation of pH\nfrom δ¹¹B. Addressing these uncertainties explicitly would strengthen the study.”\n• We now include several sentences to address this uncertainty in the Methods section\n‘Coral-Based Estimates of pCO in the Salish Sea’ in lines 622-636. We now show in this\n2\nsection (and describe below) that this is not a significant effect.\n• We assessed the temperature effect on the k value by conducting a sensitivity analysis on\nour pCO calculations. To calculate coral-based pCO in the Salish Sea, we used a\n2 2\ncarbonate chemistry solver script in python with inputs including pH (from δ¹¹B), DIC,\ntemperature and salinity. Temperature values were based on summertime averages from\nbottle data collected at the Washington Ocean Acidification Center (WOAC) station 21,\nlocated near a majority of coral sampling sites.\n• Under the assumption that temperature remained constant over the past century, we\ncalculated ∆pCO = 172 uatm. However, if we assume that historical temperatures were\n2\n1°C cooler, then ∆pCO increases slightly to 176 uatm. This temperature effect is well\n2\nwithin the uncertainty range of the coral records (+/- 41 uatm). Furthermore, if\ntemperatures have indeed warmed over the past century, our acidification estimates would\nbe even larger and more extreme. We adopt a conservative approach and assume a constant\ntemperature over the past century, and thus report ∆pCO = 172 uatm in the Salish Sea.\n2\n“While the combination of paleo and modelling approaches holds promise, the manuscript would\nbenefit from a clearer and more prominent presentation of the historical datasets. Improving\ntransparency regarding uncertainties, sampling strategies, and data handling would greatly\nenhance the robustness of the study.”\n• We thank the reviewer for recognizing our efforts to combine paleo and modeling\napproaches. Regarding the presentation of historical geochemical datasets, please refer to\nour response to the first comment above and the newly added Figure 2 to show geochemical\ndata.\n• In terms of sampling strategy, we see that Reviewer #3 also raised concerns about missing\ndetails. We agree that this description was lacking critical information and have now\nincluded additional clarity in the Methods section (lines 419-431, 434-453, and 463-481).\n• We made a concerted effort to thoroughly document and explain our choices in data\nanalysis and interpretation, including discussions on uncertainty and assumptions. We have\naddressed specific line by line comments as best as we can and hope these revisions\nenhance the clarity of the manuscript. We would be happy to provide additional\nexplanation or expand the discussion further, if helpful.\nSpecific Comments:\n“Figure 3, panel e: The description of the presented data should clarify that it represents modelled\ndata. Why are the historical coral data not included in this figure?”\n• We clarified in the figure caption that the data presented in Figure 4e represent modelled\ndata.\n• Figure 3e (now Figure 4e) shows modeled averages of seawater pCO across the CCS at\n2\nthree depth levels and three time steps. We excluded the historic coral data because the\ncorals were collected across a broad geographic and depth range with high variability in\nbackground seawater chemistry, making them unsuitable for basin-wide and depth-bin\naveraging. The variability across sites and depths can be seen by the spread in historic\npCO values along the y axis in Figure 3. Therefore, we don’t believe the coral data would\n2\n‘bin’ adequately into the regional and depth bins of Figure 4.\n“Line 15: Consider revising “the leading edge” to “a leading edge,” depending on the context.”\n• We agree with this suggestion and revised the sentence to say “a leading edge”.\n“Line 107: What about intraspecies variability, such as vital effects? This point needs\nclarification.”\n• We thank the reviewer for pointing out this information lacking in the Methods. The overall\nvital effects for this species are constrained by the calibration of Gagnon et al. (2021),\nwhich is used here for the conversion of δ¹¹B to pH. This calibration, conducted with\nmultiple individuals of corals of the same species, suggests that intraspecies variability is\nsmall compared to environmental effects. Indeed, the high precision of the Gagnon et al.\ncalibrations and the striking similarity of the slopes for environmental sensitivity between\nGagnon et al. and other cold-water coral studies support the utility of the δ¹¹B proxy. See\nfor example Supplemental Figure 13 in Gagnon et al.\n• Additionally, our comparison in the Salish Sea focuses on mean δ¹¹B values across modern\nand historic samples from the same locations. This approach helps mitigate the influence\nof individual variability and highlights broader temporal trends. Any potential intraspecies\ndifferences would be present in both modern and historical datasets, making it unlikely that\nvital effects alone explain the observed shift in mean δ¹¹B.\n• A summary of this information is now included in the Methods, Boron Isotope Anlaysis in\nlines 436-453.\n“Line 142: Specify explicitly that this refers to data from Gagnon et al. (2021).”\n• Thank you for this suggestion to improve clarity. We now explicitly reference Gagnon et\nal. 2021 in our discussion of culture conditions used to establish the δ¹¹B calibration.\n“Line 609: The sampling strategy requires further detail. This concern was raised previously by\nreviewers, yet the revisions still lack sufficient information regarding how the corals were sampled.\nE.g., which skeletal elements were sampled, distance, etc.”\n• Thank you for describing specific information that is requested regarding the sampling\nscheme. We included additional information of how the individual corals were sampled for\ngeochemical analyses in Methods, ‘Boron Isotope Analysis’ in lines 436-453.\n• Skeletal sections of ~5 mg CaCO were sampled along the primary growth axis from each\n3\ncoral using a Dremel tool approximately ~0.5-1 cm deep. Sampling is large compared to\nskeletal microstructures like centers of calcification, which we think means that the impacts\nof these features are largely averaged and homogenized across the bulk sample. This is\nsupported by the systematic trends and tight precision of even smaller samples from\nGagnon et al. (2021).\n“Additionally, potential offsets in the data could result from treatment effects (e.g., preferential\ndissolution of skeletal elements like the centres of calcification) or sampling strategies that\nselectively represent certain skeletal components. In this sense, is there any information on how\nthe historical corals were treated post-collection, such as cleaning or preservation procedures?”\n• As mentioned below and added to the text in lines 401-403, 419-431, and 436-453, samples\nincorporate a representative average of coral skeletal components by sampling broadly\nalong the full growth axis. This same sampling strategy was employed for all corals, so\nshould not influence the signals seen in our dataset. Care was also taken during cleaning\nto treat all samples identically and thus avoid preferential dissolution of specific\ncomponents.\n• All of the coral samples from the Smithsonian National Museum of Natural History were\ndried for archive after removing the coral polyp, avoiding potential issues around\npreferential dissolution that could arise from storage in solutions. Calcium carbonate is\nrelatively stable in dry environments, and the museum employs preservation methods to\nensure skeletal material remains intact. The Smithsonian implements preventative\nmeasures, including environmental regulation (ie temperature and humidity) and archive\nhandling, to maximize the long-term preservation of specimens.\n• Smithsonian Preservation Guidelines:\no https://siarchives.si.edu/what-we-\ndo/preservation#:~:text=The%20first%20and%20most%20important,the%20best\n%20rule%20of%20thumb.\n“Furthermore, as indicated by the authors, critical information is lacking for some historical\nsamples, particularly sample 7863. Why was dating not performed on this sample? Providing this\ndetail could help address gaps in the dataset.”\n• We add additional detail on these choices in Supplementary Methods 1.4 in lines 313-319,\nand also describe this additional detail below.\n• USNM 7863 was the only coral sample set lacking a recorded collection date. To address\nthis gap, we conducted research on the known collector, Ernest Quayle, to provide\ntransparency and infer unknown information (information included in Supplementary\nMethods 1.4). Quayle moved to California in 1931, collected other corals in our dataset in\n1932, and published an article on corals that same year. Based on this timeline, we infer\nthat USNM 78638, collected near San Francisco, California, was likely obtained in the\nearly 1930s. While Quayle passed away in the 1950s, providing an upper bound on\ncollection timing, a later collection date would not substantially impact the coral data, as\nthe majority of anthropogenic CO emissions occurred later in the 20th century.\n2\n• Perhaps most notably, these corals were collected from a tidepool near Moss Beach,\nCalifornia–a highly variable environment. This was the only location where modern pCO\n2\nappeared lower than historic pCO , likely due to the extreme variability of the intertidal\n2\nzone that influenced the 𝛿11B skeletal signatures. Given this high natural variability, long-\nterm signals can be obscured by environmental noise. Consequently, these data were not\nheavily weighted in our analysis or conclusions. Had they been central to our study,\nadditional efforts to constrain collection dates and reduce uncertainty would have been\nundertaken."}, {"round": 2, "reviewer_comments": {"reviewer_2": "The revisions have improved the manuscript, adding greater clarity to the methodology. The conclusions appear to be well\nsupported by the data, so I do not believe further revisions are necessary. Therefore, I am supportive of the publication of the\ncurrent version of the manuscript. I have only two minor comments that can be addressed during the final preparation:\nLine 433 – The ideas in this sentence are difficult to follow. Is \"larger\" a typo? Please revise for clarity.\nLine 460 – The comment regarding sample resolution primarily referred to the older samples. Please clarify whether any\ninformation is available about how these samples were treated after collection (e.g., whether they were bleached).", "reviewer_3": "The authors have satisfactorily addressed the previous comments and I can recommend the acceptance of the manuscript.\n(Remarks on code availability)\nI skimmed over the code but didnt run it. From what I could see, the code should be easy to run. It is accompanied by\nexplanatory text and seems well structured.", "reviewer_4": "I co-reviewed this manuscript with one of the reviewers who provided the listed reports. This is part of the Nature\nCommunications initiative to facilitate training in peer review and to provide appropriate recognition for Early Career\nResearchers who co-review manuscripts."}, "author_response": ""}]

Decision letter