Ecosystem accounting is an emerging field that aims to provide a consistent approach to analysing environment-economy interactions. One of the specific features of ecosystem accounting is the distinction between the capacity and the flow of ecosystem services. Ecohydrological modelling to support ecosystem accounting requires considering among others physical and mathematical representation of ecohydrological processes, spatial heterogeneity of the ecosystem, temporal resolution, and required model accuracy. This study examines how a spatially explicit ecohydrological model can be used to analyse multiple hydrological ecosystem services in line with the ecosystem accounting framework. We use the Upper Ouémé watershed in Benin as a test case to demonstrate our approach. The Soil Water and Assessment Tool (SWAT), which has been configured with a grid-based landscape discretization and further enhanced to simulate water flow across the discretized landscape units, is used to simulate the ecohydrology of the Upper Ouémé watershed. Indicators consistent with the ecosystem accounting framework are used to map and quantify the capacities and the flows of multiple hydrological ecosystem services based on the model outputs. Biophysical ecosystem accounts are subsequently set up based on the spatial estimates of hydrological ecosystem services. In addition, we conduct trend analysis statistical tests on biophysical ecosystem accounts to identify trends in changes in the capacity of the watershed ecosystems to provide service flows. We show that the integration of hydrological ecosystem services into an ecosystem accounting framework provides relevant information on ecosystems and hydrological ecosystem services at appropriate scales suitable for decision-making.