Estuaries are dynamic environments that are strongly affected by natural variability, as well as direct and indirect anthropogenic impacts. A better understanding of the drivers of carbon fluxes and biogeochemical variability in estuarine systems is needed, particularly with the increasing threat of ocean acidification. Morro Bay in Central California is a small nationally protected estuary, with seasonally low freshwater inputs. Since 2007, the bay has experienced a significant loss of native seagrass, Zostera marina, which is an important component of the marine ecosystem. Because seagrass photosynthesis decreases carbon dioxide and increases oxygen in the water column, the loss of seagrass has the potential to substantially change short-term carbonate chemistry and long-term carbon fluxes of an estuary. The spatial variability of carbonate chemistry was measured in Morro Bay using ship-board surveys during the low-inflow summer season and measured the temporal variability by collecting samples close to the shore from July to November. Discrete samples show an increase in total alkalinity and dissolved inorganic carbon in the mid and back bay regions, historically dominated by seagrass. Slightly lower total alkalinity and dissolved inorganic carbon were observed in the Fall season compared to the low-inflow Summer season. Analysis of the relative modification of alkalinity and dissolved inorganic carbon, paired with salinity and temperature data, contributes to an understanding of the drivers of the observed carbonate variability. This understanding may provide clues to the causes and effects of observed changes to the bay with seagrass loss. More broadly, it will inform the vulnerability of other low-inflow estuaries to future acidification and highlight the role seagrasses play in mitigating local acidification.

There is a growing need to better understand the dynamics of small and medium Mediterranean low-inflow estuaries (LIEs), which is addressed here by characterizing a heat budget and associated heat transfer processes. A one-dimensional deterministic model was developed from the advection-diffusion equation and applied to Morro Bay, CA using 15-minute water property (temperature, salinity, pressure) and meteorological (wind speed and direction, air temperature, relative humidity, air pressure, irradiance) data collected over a two-year period (2020 – 2021). Seasonal variability is observed in meteorological components, water temperature, and salinity. There is strong seasonal variability in head-mouth temperature and salinity differences. Temperature differences peak in summer (daily mean 2.52 ºC, June – Sept.). Daily average salinity difference is 0.33 (hyposaline, Sept. – Apr.) with strongest gradients observed during the winter storm season following enhanced freshwater discharge. Inverse salinity develops intermittently May – Aug. Subtidal heat flux is dominated by surface heating, whose daily average is always positive (heat input). The developed model does not quantify adequate heat export from the estuary, however, a sensitivity analysis indicates that diffusive flux may be a significant heat export component. Excess heat appears to be exported to the ocean, allowing ocean-estuary temperatures to remain similar. Characterizing estuarine dynamics like these enables us to predict how Morro Bay, and other similar estuarine systems, may respond to long and short-term environmental changes, and how these responses influence estuarine circulation and environmental health.