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Abstract Coastal ecosystems are rapidly shifting due to changes in hydrologic presses (e.g., sea‐level rise) and pulses (e.g., seasonal hydrology, disturbances, and restoration of degraded wetlands). Changing water levels and sources are master variables in coastal wetlands that can alter carbon concentrations, sources, processing, and export. Yet, how long‐term increases in water levels from marine and freshwater sources influence dissolved organic carbon (DOC) concentrations and dissolved organic matter (DOM) composition is uncertain. We quantified how long‐term changes in water levels are affecting DOC concentration (2001–2021) and DOM composition (2011–2021) differently across the Florida Everglades. DOC concentrations decreased with high water depths in peat marshes and increased with high water levels in marl marshes and across mangroves, and these relationships were reproduced in freshwater peat marshes and shrub mangroves. In the highly productive riverine mangroves, cross‐wavelet analysis highlighted variable relationships between DOC and water level were largely modulated by hurricane disturbances. By comparing relationships between water level and DOC concentrations with carbon sources from DOM fluorescence indices, we found that changing water sources between the dry and wet season shift DOM from algal to detrital sources in freshwater marshes, from detrital marsh to detrital mangrove sources in the brackish water ecotone, and from detrital mangrove to algal marine sources in downstream mangroves. As climate change and anthropogenic drivers continue to alter water levels in coastal wetlands, integrating spatial and temporal measurements of DOC concentrations and DOM compositions is essential to better constrain the transformation and export of carbon across these coastal ecosystems.