Fish ponds are, in the same time, ecosystems used for extensive fish production, which can contain significant biodiversity with rare, endemic or endangered species, and that can also play a part in climate mitigation. Indeed, fishponds, like aquatic environments as a whole, play a major role in the global carbon cycle. Anthropogenic 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. This practice aims to rejuvenate the ecosystem and mineralize the organic matter that has accumulated during the production years. However, there is a knowledge gap about its role in terms of ecosystem services (fish production, maintenance of biodiversity and carbon storage). To fil this knowledge gap, we analysed data (fish yields, abundance and diversity of primary producers, carbon storage and emissions) collected on numerous fish ponds in the Dombes region, France, since 2007. Management information, in particular the distance to the last dry-out, was collected from managers. Our results show 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. The best balance between the two primary producers is reached in the second year, where we can also observe the best fish yields. These high levels of primary producers’ abundance in the early years of the cycle enable good carbon storage through sedimentation. The dry year is marked by high emissions of greenhouse gases (CO2 and CH4), tending to make ponds sources of carbon over the entire production cycle. By encouraging the development and recolonization of the environment by macrophytes, and also by enabling an optimum unstable state of presence of the two primary producers, drying out appears to be a major agro-ecological practice, in extensive pond fish farming, structuring the functioning of the ecosystem and the services rendered. Nevertheless, drying-out a fishpond represents a major disturbance, marked by significant carbon emissions. These opposing effects will undoubtedly call for a rethinking of the hierarchy of desired ecosystem services.