The data were collected from experimental freshwater fishpond systems (semi-intensive coupled with lagoon, semi-intensive and extensive). The dataset presented is composed of: 1. Individual fish parameters (live weight, length at fork, Fulton’s condition factor (K)), at stocking and harvest for the three species reared: common carp (Cyprinus carpio), roach (Rutilus rutilus) and perch (Perca Fluviatilis), within each fishpond. 2. Overall fish performances measured in group (total live weight, number of individuals, mean live weight), at stocking and harvest, for the three species reared: common carp (Cyprinus carpio), roach (Rutilus rutilus) and perch (Perca Fluviatilis), within each fishpond 3. Physical indicators of the water quality in fishponds, weekly measured: temperature, pH, dissolved oxygen, oxygen saturation, conductivity and water transparency 4. Physical indicators of the water quality in fishponds, measured every 5 minutes on 24h once a month from May to October: temperature, pH, oxydo-reduction potential, conductivity, dissolved oxygen and oxygen saturation. 5. Concentration in pond water of chemical compounds, monthly sampled: total nitrogen (TN), ammonium, nitrite, nitrate, orthophosphate and total phosphorus(TP) 6. Concentration in pond water of chemical compounds, sampled twice on a lap time of 24h, monthly: total nitrogen (TN), ammonium, nitrite, nitrate, orthophosphate and total phosphorus(TP) 7. Concentration of chlorophyll in pond water monthly sampled: chlorophyll-a from May to October and total chlorophyll, blue chlorophyll, brown chlorophyll and green chlorophyll from May to November. 8. Concentration in TN, TC and TP in the sediment of each pond at fish stocking and harvest.