Rivers and streams export inorganic and organic carbon derived from contributing landscapes and so downstream carbon fluxes are important quantitative indicators of change in ecosystem function and for the full accounting of terrestrial carbon budgets. Carbon concentration‐discharge (C‐Q) relationships in rivers provide important information about carbon source and behavior in watersheds and are useful for estimating carbon export. However, C‐Q relationships are complex in large river systems because of spatial and temporal heterogeneity in carbon dynamics across the watershed and river networks. We quantified dissolved organic carbon (DOC) and dissolved inorganic carbon (DIC) fluxes in the Upper Mississippi River basin and investigated their relationships with land cover and hydrology. The magnitude of dissolved carbon yields ranged widely among stations, 0.6–5.7 g DOC m−2 yr−1 and 2.9–11.8 g DIC m−2 yr−1. Spatial patterns in carbon fluxes were strongly related to land cover, with agricultural sites having high DIC/low DOC exports and forested and wetland areas having the opposite. DIC was always negatively related to discharge (Q), while the DOC‐Q relationship varied with land cover. Differential behavior of carbon across the basin resulted in Q having a weak relationship with DOC and DIC at the basin outlet. Hence, there is a need to improve understanding of headwater terrestrial‐to‐aquatic carbon connections in order to improve basin‐to‐continental‐scale carbon export estimates. Our results demonstrate that quantitative understanding of carbon export by large rivers can be improved by incorporating stream network information, such as the timing, location, and source of constituent flux, rather than relying solely upon relationships between constituent behavior and seasonality or discharge at the basin outlet. Plain Language Summary Riverine carbon export is important to water quality and to fully account for regional carbon budgets. Carbon export can be estimated by observing conditions at the basin outlet. However, large river basins often have heterogeneous land cover and different areas of the basin export carbon very differently. In this study, we examined carbon export in the Upper Mississippi River Basin and in contrasting subbasins dominated by either forested/wetland or agricultural/urban land cover. We found different behavior and intensity of carbon export from the subbasins, which affected our understanding of carbon flux and dynamics at the basin outlet. This work underscores the need to integrate knowledge of subbasin behavior into studies of basin‐scale solute transport dynamics. Key Points Dissolved organic and inorganic carbon fluxes were estimated for the Upper Mississippi River Basin in north‐central USA Carbon fluxes varied strongly among land cover types with stark contrasts between agricultural areas and forested/wetland areas Accounting for spatial drivers is important for understanding carbon flux dynamics in large, heterogeneous river basins