UC Davis

Coastal carbon cycling is highly dynamic and varies across spatial and temporal scales because of interacting physical and biogeochemical processes. However, direct measurements of the carbon balance of coastal ecosystems remain limited, and their contributions to regional and global carbon budgets are still uncertain. This dissertation investigated carbon cycling in the nearshore coastal ocean and San Diego Bay using measurements of air-sea carbon dioxide (CO2) flux and carbon-related water-quality indicators. Air-sea CO2 flux was measured using eddy covariance methodology with a stationary pier-mounted tower and a mobile boat-based tower.Observations collected at the Ellen Browning Scripps Memorial Pier (hereafter Scripps Pier) from 2014-2025 indicated predominant net CO2 uptake, with a median annual flux of -85.3 mg C m-2 hr-1 (95% CI: -121.3 to -28.6). CO2 flux differed significantly among seasons, with mean uptake in spring and fall 28% greater than in summer and winter; however, the seasonal effect was small, and substantial variability occurred within seasons. No consistent diel pattern was detected, with CO2 uptake occurring throughout both day and night. No single environmental variable consistently explained CO2 flux. Instead, associations with wind speed, chlorophyll, sea surface temperature, photosynthetically active radiation (PAR), and salinity were generally weak or dependent on the temporal scale of analysis, indicating complex, scale-dependent controls on air-sea exchange. Fixed-interval median analyses reduced the influence of uneven sampling density and strengthened several apparent environmental relationships, although the resulting associations remained scale-dependent. Spatial variability in air-sea CO2 flux was evaluated using a mobile boat-based eddy covariance tower deployed throughout San Diego Bay from 2023-2025. Mean CO2 flux across the bay was -30 mg C m-2 hr-1 (95% CI: -89 to 29), indicating weak sink tendencies but no significant difference from neutral conditions during the study period. No overall difference was detected between North and South Bay when all seasons were combined because regional differences depended on season. South Bay had significantly more negative fluxes than North Bay during summer and fall, whereas no significant regional differences occurred during winter or spring. Accordingly, CO2 flux was significantly influenced by the interaction between season and bay region. Exploratory analyses identified significant associations of CO2 flux with PAR and turbidity across the bay and with pH in South Bay. These results demonstrate that whole-system averages can obscure localized and season-dependent patterns in estuarine CO2 exchange.Water quality indicators–including temperature, PAR, colored dissolved organic matter (CDOM), chlorophyll a (blue and red), pH, specific conductivity, turbidity, and dissolved oxygen–were also evaluated throughout San Diego Bay using a Manta+35 multiparameter sonde. Multivariate water-quality profiles did not differ significantly between North and South Bay, indicating that the bay was structured by continuous spatial gradients rather than distinct regional divisions. Seasonal variability was the dominant source of multivariate variation, with CDOM, temperature, and dissolved oxygen contributing most strongly. In contrast, individual variables exhibited significant spatial differences, with the strongest regional effects occurring for pH, CDOM, and temperature. Overall, water-quality conditions were generally comparable to those reported for other temperate estuaries, despite clear gradients in organic matter and indicators related to productivity. Collectively, these studies demonstrate that resolving the role of dynamic coastal ecosystems in carbon cycling requires long-term observations together with spatially and seasonally resolved measurements of air-sea CO2 exchange and associated environmental variables.