Freshwater marshes are well-known for their ecological functions in carbon sequestration, but complete carbon budgets that include both methane (CH4) and lateral carbon fluxes for these ecosystems are rarely available. To the best of our knowledge, this is the first full carbon balance for a freshwater marsh where vertical gaseous (carbon dioxide (CO2) and CH4) and lateral hydrologic fluxes (dissolved and particulate organic carbon) have been simultaneously measured for multiple years (2011-2013). Carbon accumulation in the sediments suggested that the marsh was a long-term carbon sink and accumulated ~96.9±10.3 (±95% CI) g C m−2 yr−1 during the last ~50 years. However, abnormal climate conditions in the last three years turned the marsh to a source of carbon (42.7±23.4 g C m−2 yr−1). Gross ecosystem production and ecosystem respiration were the two largest fluxes in the annual carbon budget. Yet, these two fluxes compensated each other to a large extent and led to the marsh being a CO2 sink in 2011 (−78.8±33.6 g C m−2 yr−1), near CO2-neutral in 2012 (29.7±37.2 g C m−2 yr−1), and a CO2 source in 2013 (92.9±28.0 g C m−2 yr−1). The CH4 emission was consistently high with a three-year average of 50.8±1.0 g C m−2 yr−1. Considerable hydrologic carbon flowed laterally both into and out of the marsh (108.3±5.4 and 86.2±10.5 g C m−2 yr−1, respectively). In total, hydrologic carbon fluxes contributed ~23±13 g C m−2 yr−1 to the three-year carbon budget. Our findings highlight the importance of lateral hydrologic inflows/outflows in wetland carbon budgets, especially in those characterized by a flow-through hydrologic regime. In addition, different carbon fluxes responded unequally to climate variability/anomalies and, thus, the total carbon budgets may vary drastically among years.This article is protected by copyright. All rights reserved.