<p>Climate change is expected to significantly alter carbon dynamics in coastal ecosystems like salt marshes. However, our capacity to detect and respond to these changes is limited by insufficient knowledge of baseline ecosystem metabolism across aquatic ecosystems. Quantifying metabolic rates—gross primary production (GPP), ecosystem respiration (ER), and net ecosystem metabolism (NEM)—reveals whether an ecosystem stores (net autotrophic) or releases (net heterotrophic) carbon. Few studies have monitored water quality at high frequency over full annual cycles in marsh-dominated estuaries, limiting estimates of seasonal metabolic variation. In this study, we examined the metabolic balance of a salt marsh channel in coastal New Jersey, an area heavily impacted by human activities and experiencing rapid sea level rise. Over three years, we monitored environmental parameters—salinity, temperature, dissolved oxygen, pH, turbidity, and chlorophyll <i>a</i>—at three sites within the channel. Using these data, we calculated metabolic rates and assessed relationships between environmental conditions and metabolism, including impacts of storm events. Results revealed an overall net heterotrophic system (mean NEM: -29.5 ± 15.5 mmol O₂ m^− 2 d^− 1) with high seasonal variation ranging from slightly net autotrophic in winter/early spring (February maximum: 12.0 ± 6.9 mmol O₂ m^− 2 d^− 1) to net heterotrophic in late spring/fall (September minimum: -88.1 ± 24.9 mmol O₂ m^− 2 d^− 1). Temperature played a dominant role in metabolic dynamics, while storms temporarily intensified heterotrophic conditions. Our findings reveal seasonal patterns in productivity and respiration that affect carbon storage capacity and document natural ecosystem variability and responses to disturbances—insights critical for understanding how these vital blue carbon systems may respond to environmental changes.</p>