As aquaculture production is increasing considerably, it needs to become more environment-friendly. Based on a participatory process, an ecologically intensive pond system was designed to test three hypotheses: a combination of intensive and extensive areas provides more ecosystem services than an intensive or extensive area alone; coupling a planted lagoon with an intensive pond decreases the latter's environmental impacts and maintains or increases its fish productivity; and using formulated feed in polyculture increases growth of all fish species. To test these hypotheses, we designed a specific integrated multi-trophic aquaculture system composed of a polyculture of common carp (Cyprinus carpio), roach (Rutilus rutilus) and tench (Tinca tinca) and a lagoon planted with macrophytes to filter the water. This pond system was compared with “extensive” (unfed) and “semi-intensive” fishpond systems without a planted lagoon. We measured fish growth performances, water quality, chlorophyll concentrations and water and sediment nutrient contents. We also calculated the mass balance of nutrients. Concentrations of total nitrogen and phosphorus increased in sediments, indicating that nutrients were stored in the ponds, especially in planted lagoon; the planted lagoon decreased phytoplankton development, and limited blooms, but it slightly decreased fish growth performances compared to those in semi-intensive fishponds. The formulated feed supplied clearly increased fish growth performances and the survival rate, and seemed also to increase the use of available nutrients in ponds, which improved the production of overall fish biomass. In conclusion, the planted lagoon provides ecosystem services on nutrients cycling and habitat for natural biodiversity. Improving knowledge about nutrient cycles from formulated feed within the pond food web would be useful to increase the amounts of nutrients converted into fish biomass.