The development of complete regional carbon (C) budgets for different biomes is an integral step in the effort to predict global response and potential feedbacks to a changing climate regime. Wetland and lake contributions to regional C cycling remain relatively uncertain despite recent research highlighting their importance. Using a combination of field surveys and tower-based carbon dioxide (CO2) flux measurements, modeling, and published literature, we constructed a complete C budget for the Northern Highlands Lake District in northern Wisconsin/Michigan, a ∼6400 km2 region rich in lakes and wetlands. This is one of the first regional C budgets to incorporate aquatic and terrestrial C cycling under the same framework. We divided the landscape into three major compartments (forests, wetlands, and surface waters) and quantified all major C fluxes into and out of those compartments, with a particular focus on atmospheric exchange but also including sedimentation in lakes and hydrologic fluxes. Landscape C storage was dominated by peat-containing wetlands and lake sediments, which make up only 20% and 13% of the landscape area, respectively, but contain >80% of the total fixed C pool (ca. 400 Tg). We estimated a current regional C accumulation of 1.1±0.1 Tg yr−1, and the largest regional flux was forest net ecosystem exchange (NEE) into aggrading forests for a total of 1.0±0.1 Tg yr−1. Mean wetland NEE (0.12±0.06 Tg yr−1 into wetlands), lake CO2 emissions and riverine efflux (each ca. 0.03±0.01 Tg yr−1) were smaller but of consequence to the overall budget. Hydrologic transport from uplands/wetlands to surface waters within the region was an important vector of terrestrial C. Regional C fluxes and pools would be misrepresented without inclusion of surface waters and wetlands, and C budgets in heterogeneous landscapes open opportunities to examine the sensitivities of important fluxes to changes in climate and land use/land cover.