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Climate and human modifications, including restoration, are changing freshwater availability in wetland ecosystems. Changes in spatiotemporal variability in water depth can influence biogeochemistry and aquatic metabolism (net ecosystem productivity, gross primary productivity [GPP], and ecosystem respiration [ER]). In subtropical wetlands, flocculent organic matter (floc) is a dominant form of organic matter made up of periphyton, macrophytes, and microbes. How changes in water depth with climate and human modifications of subtropical wetlands influence biogeochemistry and the metabolism of floc is uncertain and necessary to understand the consequences for carbon (C) cycling. We collected seasonal floc samples from shorter‐hydroperiod marshes (Taylor Slough Panhandle [TS/Ph]) and longer‐hydroperiod marshes (Shark River Slough [SRS]) in Everglades National Park (Florida, U.S.A.). We measured floc‐specific metabolism and biogeochemistry during the wet (May–November) and dry seasons (December–April) when marsh conditions differed in water depth, photosynthetically active radiation (PAR), floc chlorophylla, bulk density, and C and nutrients. Floc biogeochemistry was driven by hydrologic changes in water depth, while floc metabolism was influenced by floc biogeochemistry and PAR in both marshes. Floc‐specific metabolism was more net heterotrophic (GPP < ER) in TS/Ph than in SRS, driven by floc bulk density, total nitrogen, total C, total phosphorus, and total inorganic C. Increasing water depths with freshwater restoration may drive higher rates of C loss in shallower compared to deeper marshes. Understanding how hydrologic changes affect organic matter lability and respiration is important in managing C storage in ecosystems.