In times of the Anthropocene, securing the provision and access to key ecosystem services (water quality, carbon storage, biodiversity habitat etc.) and taking into account the associated benefits, risks and responsibilities is a challenge that requires the design of innovative conceptual and practical frameworks able to connect multiple organizations and institutions together. We suggest that this challenge can be framed as an accounting issue. We argue that important insights can be drawn from accounting research, which is traditionally focused on the management of firms, and applied to the field of environmental governance. From a theoretical standpoint, accounting research typically addresses questions such as: who is accountable to whom in the context of an organized collective action, what information (economic, biophysical etc.) should be provided to which decision-maker, when, to support what type of action and to contribute to the effective resolution of what specific problems? Furthermore, from a practical standpoint, accounting provides a diversity of concepts and techniques useful to gather, treat and modelize information, actions and resources within and across organizations (credit/debit, manageables, allocation keys, balance sheets, costs etc.). In this paper, we will present results of our work on a French water services company – Lyonnaise des Eaux – involved with various stakeholders (farmers, municipalities, NGOs etc.) in the shared governance of ecosystem services and biodiversity in several locations in France. In our case studies, there is never a single supervising institution that has the overall authority to solve the corresponding agency and accountability issues, which thus calls for the emergence of a trans-organizational governance. We will address this challenge by using insights from accounting research to suggest an original accounting framework useful for the company and other stakeholders, and specifically designed to contribute to the organization of collective responsibilities over the management of ecosystem services in these locations.