As the climate continues to warm, wildfires are expected to increase in frequency and severity, particularly across the western United States, likely impacting the global carbon (C) balance. Fire influences C stocks via shifts in vegetation, hydrologic flow paths, and microbial communities. These disturbances alter C partitioning across landscapes, connectivity between hillslopes and streams, and microbial function. However, potential linkages between disturbance, C cycling, and terrestrial and aquatic microbiomes require further investigation. This study explored the long-term legacy of wildfire on watershed C dynamics and aquatic microbial communities, while evaluating how changes to the terrestrial landscape are reflected in stream systems. During the summer of 2019, dissolved inorganic and organic carbon pools were measured along with estimates of stream metabolism and characterization of aquatic microbiomes for three streams draining catchments that burned during the 2002 Colorado wildfire season and two streams unaffected by fire. Compared to unburned watersheds, aquatic C exports and microbiomes were characteristically different in burned watersheds; specifically, C stocks were less aromatic and less bioavailable, which could exert controls on microbial communities. Although stable isotope analyses revealed that all streams were dominated by allochthonous sources, trends in dissolved C pool composition in streams draining unburned landscapes suggest shifting flow paths and/or differences in in-situ sources and transformation between watersheds. Overall, wildfire appears to create a feedback loop between C quality, processing, and microbiomes due to changes in vegetation and hydrology in the terrestrial environment as well as differences in microbiomes across the landscape. These alterations could affect recovery dynamics in burn scars and imply that wildfires in warmer, drier climates could result in steady state shifts.