Agroecology largely focusses on terrestrial agroecosystems, but it can also be applied to fish farming. Indeed, ponds are typically used for fish production in Europe, but are also important reservoirs of biodiversity. Numerous studies demonstrate that both fish production and biodiversity are strongly determined by human management. One key practice in extensive fish farming, although more rare in Europe, is to dry out ponds. They are left dry for a complete year after several years of fish production. However, the extent to which this practice affects the functioning of the ecosystem, its biodiversity and fish production remain unclear. We investigated data from 85 fish ponds in the Dombes region, France, sampled between 2007 and 2014. We related variation in key abiotic characteristics to the time since last dry out. The dataset included organic matter content in pond sediments and concentrations of inorganic nitrogen and phosphorus in the water column, and biotic components such as macrophytes cover and richness, phytoplankton concentration and richness, macroinvertebrates density, and fish yield. Our results show that drying out facilitates the mineralization of organic matter in sediments and results in higher concentrations of inorganic nitrogen in the water column. Macrophytes cover is highest during the first year after drying out, and gradually declines after at the expense of increasing phytoplankton concentration. The diversity of both is highest in the first year after drying out and declines rapidly, especially for macrophytes. Fish yield is at its maximum in the second year. Drying out fish ponds appears to be an important agroecological practice in extensive fish farming with an application every three to four years. By nutrient recycling, this practice has a positive impact on the balance between primary producers and indirectly on the whole food web during two years. It optimizes fish production and allows biodiversity conservation.