Drivers of Ecosystem Metabolism in an Anthropogenically Modified Delta

Estuaries are under threat globally from a wide range of stressors, with rates of ecosystem metabolism - respiration (R), gross primary production (GPP), and net ecosystem metabolism (NEM) - representing a way for resource managers to quantify their impacts. In this study, we assessed how natural and anthropogenic stressors have altered metabolism within the extensively modified Sacramento-San Joaquin Delta ("Delta") in California, USA. Metabolism was estimated using a diel open-water technique utilizing dissolved oxygen measurements from a high frequency (15 min) water quality monitoring array, and spanned 6 sites across 11 years (2014-2025). Our analyses were driven by a conceptual model of Delta carbon (C) cycling focused on 1) Invasive aquatic vegetation (IAV), 2) Phytoplankton, 3) Wastewater treatment plant (WWTP) upgrades, 4) Large-scale flow alterations, and 5) Wet vs. dry years. We found that allochthonous C fuels net heterotrophy in the outer riverine sections of the Delta, while the heavily vegetated central Delta produces autochthonous C remineralized elsewhere in the system. IAV were the dominant primary producers, with low phytoplankton production except during a historic bloom. WWTP upgrades imparted negligible changes to metabolism, with low chlorophyll a (< 5 µg L^-1) both before and after. Introduction of a flow barrier - a management response to drought - hydrodynamically isolated deep-water channels from nearby shallow areas, resulting in decreased metabolism indicative of changes to C transport. Contrary to past research, low rainfall years were associated with increased metabolism. This study demonstrates how multi-sensor arrays can be used to quantify ecosystem responses to major environmental stressors.

The online version contains supplementary material available at https://doi.org/10.1007/s12237-026-01833-z.