pH in the South Slough Estuary

Issue Summary:

pH in the ocean has been dropping for many years (ocean acidification) but for at least the past 16 years, pH has been rising in the South Slough estuary.

Why do we care:

pH affects how marine organisms access nutrients, and how they reproduce and grow (e.g., shells and skeletons do not form as well at lower ocean pH levels). Changes in pH in estuary waters have received much less attention than ocean pH. The causes for rising pH in our estuary are unknown.

Red Circles indicate System Wide Monitoring Program Stations.

What’s Happening?

Our analyses of 8 years of pH data (2002-2010) from the South Slough Reserve’s 4 long term water quality monitoring stations reveal that pH in the estuary is increasing. While the rise in estuary water pH is surprising because it is the opposite direction of what is happening in the ocean (decreasing pH), the data showed high variability, both between stations along the estuarine gradient and over time (tidally, seasonally, and annually). The greatest increases in pH occurred near the mouth of South Slough and in the mid region of the estuary near Valino Island (Figure 1). Overall lower pH values occurred in the freshwater part of the estuary (Winchester Creek and Sengstacken), as expected since fresh water is naturally more acidic than seawater.

Figure 1. Long term water quality monitoring SWMP data reveal pH Trends

As part of our analyses. we looked for correlations between the pH data & long term ocean and climate cycles. The station located nearest the mouth of the estuary (Charleston Bridge) lacked any correlation to indices that indicate an ocean derived source for the higher pH waters suggesting that the pH rise in South Slough is probably due more to estuarine-scale processes (such as primary productivity). However, the pH trends at the mid estuary and freshwater sites (Valino Island and Winchester Creek) did show correlation to an index that measures climate variability. This indicates watershed inputs and local climate variability. These conflicting explanations illustrate the complexity of the system, and indicate that the chosen indices and/or components of future analyses should be modified to include shorter-term variability and additional ecosystem and watershed scale variables

Figure 2. Long term water quality monitoring SWMP data reveal increasing pH trends

Why Is It Happening?

Several ecological processes potentially contribute to the observed shifts in pH values within the South Slough estuary. These factors and processes include: (1) increased partial pressure of Carbon dioxide gas (pCO2), ocean acidification, and changes in ocean carbonate chemistry; (2) regional shifts in precipitation, freshwater inputs, and salinity; (3) sea level rise and coastal inundation; (4) photosynthesis and respiration by estuarine phytoplankton, benthic algae, seagrasses, and salt marsh plants; and (5) denitrification and sulfate reduction in hypoxic estuarine habitats.

A fifth factor that may help explain increased estuarine pH values in the South Slough estuary is the relationship between Net Ecosystem Metabolism (NEM) and pH. NEM is the net effect of biological production and respiration for the estuary and helps determine whether an estuarine environment is a source or sink of carbon. When production exceeds respiration, NEM is positive which suggests the ecosystem is a carbon source. When respiration exceeds production, NEM is negative which suggests the ecosystem is a carbon sink- it uses more carbon that it produces. The relationship between carbon dioxide and pH is not fully understood; however, when carbon dioxide dissolves in seawater, it forms an acid, which ultimately lowers pH.

A study was conducted at 22 National Estuarine Research Reserves/42 sites, including 2 sites in South Slough to analyze production, respiration, & net ecosystem metabolism (NEM) rates. One important result showed that metabolic rates were influenced by the adjacent habitat (SAV, marsh, open water, or mangrove) (Caffrey 2003). Only 3 sites out of 42 showed positive mean annual NEM rates (carbon source), and they were located near eelgrass beds (SAV) or above macroalgae mats, whereas the other 3 sites near eelgrass beds (SAV) had slightly negative NEM rates (carbon sink); however, they showed a positive NEM rate in at least one season. The results of this study along with local eelgrass monitoring results may contribute to explaining the observed trend in increased estuarine pH values in South Slough if the overall system is dominated by production rather than respiration. If eelgrass beds are abundant and productive, these sites & potentially the South Slough estuary is operating as a carbon source, which would drive pH up.

What’s Being Done?

Very little is known about the inherent variability in the dissolved carbon dioxide (pCO2) concentrations in nearshore marine waters, and the relationships between ocean acidification and pH values are poorly understood for Pacific coast estuaries. Long-term datasets generated by the National Estuarine Research Reserve – System-Wide Monitoring Program (SWMP) provide an ideal opportunity to analyze variability over space and time in estuarine water parameters, and to identify possible directional changes in pH values as a variable that is potentially responsive to changes in ocean carbonate chemistry and changes in ecological conditions inside the estuaries. Using the existing dataset to establish a baseline of estuary pH, continuing to monitor pH as well as explore differences and correlation between different pH measuring.


Ocean acidification is the term used to describe the decrease in the pH levels of the world’s oceans. The lower the pH level the more acidic the water. Scientists estimate that the ocean is 25-30 % more acidic today than it was 300 years ago.

pH is a measure of the acidity or “basicity” of an aqueous solution and ranges from a scale of 0 to 14. Pure water is said to be neutral, with a pH close to 7.0 at 25 °C (77 °F). Solutions with a pH less than 7 are said to be acidic and solutions with a pH greater than 7 are basic or alkaline. Since the scale (0 to 14) is logarithmic, each number represents a 10 fold change in the pH of the water. A solution with a pH of 6 is 10 times more acidic than one with a pH of 7.
Figure 3. pH levels showing the range from acidic to basic with neutral at pH 7.
pH affects many chemical and biological processes in the water. Different organisms require different ranges of pH to function. Because they require a highly specific pH range, their physiological processes may be adversely affected by changes in the pH of their environment. Most organisms function in a narrow pH range of 6.5 to 8. At low pH (pH 6.0), fish may develop damage to the gills, skin and eyes. Under eutrophic conditions (too many nutrients); pH can influence the formation of harmful algal blooms where algal species with tolerance to extreme pH levels grow and dominate the community.

Changes in pH can also have indirect impacts on aquatic organisms. For example, changes in pH can alter the biological availability of metals, the speciation of nutrients and the toxicities of ammonium, aluminum and cyanide. The solubility of heavy metals determines the level of toxicity; at low pH they are more soluble and tend to be more toxic. Increases in pH can also cause the electrostatic forces that bind viruses to particles to be overcome, thus facilitating their release to the water column. pH is important in calcium carbonate solubility, which is important for shell-forming organisms. Shell growth (i.e. calcification) is inhibited if water becomes too acidic.

Carbon dioxide from the atmosphere dissolves in seawater, CO2 reacts with water, H2O, to form carbonic acid, H2CO3: CO2 + H2O ↔ H2CO3. Carbonic acid dissolves rapidly to form H+ ions (an acid) and bicarbonate, HCO3-(a base). Seawater is naturally saturated with another base, carbonate ion (CO3−2) that acts like an antacid to neutralize the H+, forming more bicarbonate.
Figure 4. Chemistry of seawater depicting net reaction
of ocean acidification (PMEL Carbon Group)
The net reaction is: CO2 + H2O + CO3−2→ 2HCO3- As the carbonate ions become depleted, the concentrations of important calcium carbonate minerals in seawater decline. These minerals are required by organisms, such as corals and some algae, for building shells. Additional effects of ocean acidification include alteration in reproduction, physiological biology, food resources, changes in acoustic properties of seawater, and decrease in burial rate of carbonate sediments.

The link between ocean acidification and estuary pH is complex.

Recent oceanographic measurements reveal that acidified seawater is currently upwelling close to the Pacific continental shelf of Oregon, Washington, and northern California. The acidified waters presumably move by advective transport into estuaries where they may have corrosive impacts on larvae and juveniles of oysters and other bivalves. This presumption is problematic, however, because it is not clear how directly or indirectly the carbon cycling, pH, and total alkalinity of estuarine habitats are influenced by the carbonate chemistry of the nearshore ocean. Carbon cycling in estuaries is a complex process that is closely linked to daily and seasonal changes in tides, salinity, temperature, dissolved oxygen concentrations, photosynthesis, respiration, nutrient availability, and denitrification. In the face of current declining ocean conditions, however, it is critical to establish baseline pH records. Nearshore environments may be affected most severely by the ecological, physical, and socioeconomic effects of ocean acidification. This has an impact on the delivery of marine-based ecosystem services, which over half of the world’s population depend on and potentially could result in billions of dollars in lost income/products. Understanding additional stressors on coastal and estuarine ecosystems may help to reduce threats to coastal resources, providing economic benefits from the ocean and ecosystem resilience.