The use of digestates as a nutrient-rich by-product of biogas productionas cheap fertilizers in agriculture is experiencing an important increase in the European Union. The growth of digestate markets is promoted as a tool to develop a circular bioeconomy in rural areas. However, regional and local conflicts around digestates use are on the rise, due to potential negative externalities. One of the major externalities lies in the fear of nitrates, phosphates and pathogens pollution of water resources. These conflicts threaten the very existence of digestate markets. The recent literature on circular economy emphasizes the importance of regional governance for circular economy implementation and success in rural territories. By governance, we understand here the coordination of stakeholders to organize economic activity. The aim of this paper is therefore to understand the role of the regional coordination of stakeholders to manage conflicts affecting digestate markets in situations of information asymmetry or shared uncertainty. We present in this article the regional governance of two antagonistic case studies of digestate markets in France. We mirror the two cases as one is experiencing severe conflicts over the protection of water resources with a poor regional coordination of stakeholders, and the second one is experiencing almost no conflict as digestate use has been designed and implemented through intense regional coordination in order to help protecting the water resources. We identify regional and sub-regional governance mechanisms and we analyse their success or their failure in preventing and managing conflicts over water resources protection.