Fish ponds are, in the same time, ecosystems used for extensive fish production and contain significant biodiversity with rare, endemic or endangered species. Man-made pond in origin, their functioning is mainly influenced by management practices. One such practice is drying-out, which consists to drain the pond for an entire production season, to cause a disturbance of the ecosystem and mineralize the accumulated organic matter. However, there is a knowledge gap about its role in terms of ecosystem services. We analysed data (fish yields, abundance and diversity of primary producers) collected on 134 fish ponds in the Dombes region, France, since 2007. Management information, fertilization, liming and in particular the distance to the last dry-out, was collected from managers. Our results showed that the dry out year allowed a recolonization of aquatic plants during the first year with water, with levels of diversity and cover at their highest while the phytoplankton concentration is at its minimum. They are decreasing during the following wet years, in parallel with an increase in algae. From a fish production point of view, the best fish yields were observed the second year, where a balance between the two primary producers was reached. By encouraging the development and recolonization of the environment by macrophytes, and by enabling the presence of the two primary producers, drying out appears to be an important agro-ecological practice, in extensive pond fish farming, structuring the functioning of the ecosystem and the services rendered (fish production, promotion of biodiversity but also carbon storage).