The hydrology of coastal ecosystems is rapidly changing in response to both the ongoing press of sea-level rise, and repeated pulse events. Changing water depths can alter subsidies and stressors to coastal ecosystems, and ecological responses likely depends on the relative change in dissolved organic matter (DOM) concentrations and composition. We analyzed 20 years of water depth, total nitrogen, total phosphorus, dissolved organic carbon (DOC), and bacterioplankton productivity and 12 years of DOM fluorescence data to understand how freshwater and marine hydrologic pulses affect the production, transport, and processing of DOM in the marsh, ecotone, and mangroves of Everglades wetlands. Both water depths and total phosphorus increased throughout the Everglades in the past 20 years. Total nitrogen and bacterioplankton productivity were more variable between sites, and DOC concentrations have not changed over time. Sources of DOM shifted from dry to wet season in each region of the Everglades: from algal to detrital sources in the freshwater marsh, between marsh and mangrove sources in the ecotone, and between mangrove and marine sources in the downstream mangroves. Cross-wavelet analysis of water depth showed a strong relationship between DOC concentration and water depth at sources of detrital carbon: a negative relationship in the peat marsh of Shark River Slough (SRS), and a positive relationship in the shrub mangroves of Taylor Slough/Panhandle (TS/Ph). Across the Everglades average values of the Fluorescence Index across decreased from 1.533 to 1.519 from 2012 to 2021, indicating a decrease in microbial processing of DOM. The shifts in carbon source and processing that we present evidence for will have significant repercussions for the fate of carbon stored in the Everglades, and indicate that both sea-level rise and restoration are changing the fate of carbon produced, and transported through the Everglades.