The Energy Independence and Security Act of 2007 (EISA), Section 712, authorizes the U.S. Department of the Interior to develop a methodology and conduct an assessment of the Nation's ecosystems focusing on carbon stocks, carbon sequestration, and emissions of three greenhouse gases (GHGs): carbon dioxide, methane, and nitrous oxide. The major requirements include (1) an assessment of all ecosystems (terrestrial systems, such as forests, croplands, wetlands, shrub and grasslands; and aquatic ecosystems, such as rivers, lakes, and estuaries), (2) an estimation of annual potential capacities of ecosystems to increase carbon sequestration and reduce net GHG emissions in the context of mitigation strategies (including management and restoration activities), and (3) an evaluation of the effects of controlling processes, such as climate change, land use and land cover, and wildlfires. The purpose of this draft methodology for public review is to propose a technical plan to conduct the assessment. Within the methodology, the concepts of ecosystems, carbon pools, and GHG fluxes used for the assessment follow conventional definitions in use by major national and international assessment or inventory efforts. In order to estimate current ecosystem carbon stocks and GHG fluxes and to understand the potential capacity and effects of mitigation strategies, the method will use two time periods for the assessment: 2001 through 2010, which establishes a current ecosystem GHG baseline and will be used to validate the models; and 2011 through 2050, which will be used to assess future potential conditions based on a set of projected scenarios. The scenario framework is constructed using storylines of the Intergovernmental Panel on Climate Change (IPCC) Special Report Emission Scenarios (SRES), along with initial reference land-use and land-cover (LULC) and land-management scenarios. An additional three LULC and land-management mitigation scenarios will be constructed for each storyline to enhance carbon sequestration and reduce GHG fluxes in ecosystems. Input from regional experts and stakeholders will be solicited to construct realistic and meaningful scenarios. The methods for mapping the current LULC and ecosystem disturbances will require the extensive use of both remote-sensing data and in-situ (for example, forest inventory data) to capture and characterize landscape-change events. For future potential LULC and ecosystem disturbances, key drivers such as socioeconomic, policy, and climate assumptions will be used in addition to biophysical data. The product of these analyses will be a series of maps for each future year for each scenario. These annual maps will form the basis for estimating carbon storage and GHG emissions. For terrestrial ecosystems, carbon storage, carbon-sequestration capacities, and GHG emissions under the current and projected future conditions will be assessed using the LULC and ecosystem-disturbance estimates in map format with a spatially explicit biogeochemical ensemble modeling system that incorporates properties of management activities (such as tillage or harvesting) and properties of individual ecosystems (such as elevation, vegetation characteristics, and soil attributes). For aquatic ecosystems, carbon burial in sediments and GHG fluxes are functions of the current and projected future stream flow and sediment transports, and therefore will be assessed using empirical modeling methods. Validation and uncertainty analysis methods described in the methodology will follow established guidelines to assess the quality of the assessment results. The U.S. Environmental Protection Agency's Level II ecoregions map (which delineates 24 ecoregions for the Nation) will be the practical instrument for developing and delivering assessment results. Consequently, the ecoregion will be the reporting unit of the assessment because the mitigation scenarios, assessment results, validation, and uncertainty analysis will be