The System of Environmental-Economic Accounting – Ecosystem Accounting (SEEA-EA) is a spatially-based, integrated statistical framework for organizing biophysical information about ecosystems, measuring ecosystem services (ES). Water flow regulation ES and biophysical modeling are among the main topics in the individual ES part of the SEEA-EA framework and flood regulation ES is one of the important services. Characterizing and assessing flood regulation is a challenging task as both assessment and accounts of this ES need various data which are usually not available through direct or indirect measurements, therefore modeling approaches of water regulation are much needed. Despite growing attention and studies using hydrologic models to assess and/or map flood regulation ES, the accounting of this service is still not well developed. In this paper, we present an approach for accounting flood regulation at a local scale using ArcSWAT modeling. It is based on the results of flood regulation ES assessment, where modeling results are used to quantify the ES indicators and delineate the service providing areas (SPA) and service demand areas (SDA). The actual flow of flood regulation is calculated as a ratio between ES demand and ES potential and it represents the area of SPA which corresponds to the demand for flood regulation represented by SDA. The results show that predominant flood regulations ES supply is provided by the forest ecosystem as well as the actual flow. The accounting of flood regulation is strongly determined by ecosystem extent mapping. The CORINE Land Cover (CLC) provides the most appropriate and available data for mapping ecosystem extent at smaller scales. However, at a larger scale, it is too coarse and the combination of Mapping and Assessment of Ecosystems and their Services (MAES) national ecosystem mapping gives better results.