Most approaches to estimate ecological value use monetary valuation. Here, we propose a different framework accounting ecological value in biophysical terms. More specifically, we are implementing the ecosystem natural capital accounting framework as an operational adaptation and extension of the UN System of Economic and Environmental Accounting/Ecosystem Accounting. The proof-of-concept study was carried out at the Rhône river watershed scale (France). Four core accounts evaluate land use, water and river condition, bio-carbon content of various stocks of biomass and its uses, and the state of ecosystem infrastructure. Integration of the various indicators allows measuring ecosystems overall capability and their degradation. The 12-year results are based on spatial–temporal geographic information and local statistics. Increasing levels of intensity of use are registered over time, that is, the extraction of resources surpasses renewal. We find that agriculture and land artificialisation are the main drivers of natural capital degradation.