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Abstract Dissolved organic and inorganic carbon (DOC and DIC) influence water quality, ecosystem health, and carbon cycling. Dissolved carbon species are produced by biogeochemical reactions and laterally exported to streams via distinct shallow and deep subsurface flow paths. These processes are arduous to measure and challenge the quantification of global carbon cycles. Here we ask: when, where, and how much is dissolved carbon produced in and laterally exported from the subsurface to streams? We used a catchment‐scale reactive transport model, BioRT‐HBV, with hydrometeorology and stream carbon data to illuminate the “invisible” subsurface processes at Sleepers River, a carbonate‐based catchment in Vermont, United States. Results depict a conceptual model where DOC is produced mostly in shallow soils (3.7 ± 0.6 g/m²/yr) and in summer at peak root and microbial respiration. DOC is flushed from soils to the stream (1.0 ± 0.2 g/m²/yr) especially during snowmelt and storms. A large fraction of DOC (2.5 ± 0.2 g/m²/yr) percolates to the deeper subsurface, fueling deep respiration to generate DIC. DIC is exported predominantly from the deeper subsurface (7.1 ± 0.4 g/m²/yr, compared to 1.3 ± 0.3 g/m²/yr from shallow soils). Deep respiration reduces DOC and increases DIC concentrations at depth, leading to commonly observed DOC flushing (increasing concentrations with discharge) and DIC dilution patterns (decreasing concentrations with discharge). Surprisingly, respiration processes generate more DIC than weathering in this carbonate‐based catchment. These findings underscore the importance of vertical connectivity between the shallow and deep subsurface, highlighting the overlooked role of deep carbon processing and export.