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How climate and habitat drive variation in aquatic metabolism in wetlands remains uncertain. To quantify differences in seasonal aquatic metabolism among wetlands, we estimated aquatic ecosystem metabolism (gross primary productivity, GPP; ecosystem respiration, ER; net aquatic productivity, NAP) in subtropical ridge and slough wetlands of the Florida Everglades from more than 2 yr of continuously measured water column dissolved oxygen, photosynthetically active radiation (PAR), water temperature, and water depth. Gross primary productivity and ER were modeled from light, temperature, and water depth using non-linear minimization and maximum likelihood. Reaeration rates were estimated from wind speed. Dissolved oxygen was below saturation at all sites during both wet and dry seasons. Water depth interacted with vegetation to influence PAR, water temperature, and spatiotemporal patterns in aquatic metabolism. Gross primary productivity and ER were highest at the slough with lowest submerged aquatic vegetation (low-SAV slough), intermediate in the sawgrass (Cladium jamaicense) ridge site, and lowest at the slough with highest submerged aquatic vegetation (high-SAV slough). Ecosystem respiration was strongly positively correlated with GPP at the sawgrass ridge and low-SAV slough sites. Gross primary productivity increased with water temperature and PAR across all habitat types, whereas ER decreased (more respiration) with water temperature and PAR. Net aquatic productivity was negatively correlated with water temperature and positively correlated with PAR, suggesting that ER was more sensitive than GPP to water temperature. Aquatic metabolism was largely net heterotrophic in all wetlands, and high-SAV appeared to buffer seasonal variation in PAR and water temperatures that drive NAP in subtropical wetlands. Our results suggest that aquatic ecosystem metabolism in wetlands with seasonal hydrology is sensitive to changes in water depth and vegetation density that influence temperature and light. Expanding our understanding of how metabolic processes and carbon cycling in wetland ecosystems vary across gradients in hydrology, vegetation, and organic matter could enhance our understanding and protection of conditions that maximize carbon storage.