Ctenopharyngodon idella and Pelteobagrus fulvidraco are considered as two economically important aquaculture species in China with the largest production. The sediment-water interface in aquatic systems is a bridge connecting bottom sediments with the overlying water column. The transition zone between oxygenated overlying water and anoxic, or anaerobic, sediments forms over a gradient of just a few millimeter sand and can easily be disturbed by mechanical mixing (bioturbation). To determine the seasonal variance of nitrogen and phosphorus exchange in different aquaculture model ponds and explore the relationship between nitrogen and phosphorus fluxes and environment factors of overlying water in two polyculture systems, C. idella and P. fulvidraco aquaculture models ponds, we studied by in situ Observation device of nutrient flux in sediment-water interface from April to October of 2013. In situ experiments, benthic fluxes of nutrients at the sediment-water interface were measured, and its related factors were analyzed. During our experiment, nitrate, nitrite and TN were taken up by sediment in the beginning of the culture period (from Apr. to Jun.), while it changed to release from sediments to water in the middle and later stages of the culture period. Meanwhile, fluxes of PO₄^3- and TP presented the similar trends. Results also showed that the differences of concentration variation range of NO₂^--N, NO₃^--N and PO₄^3--P were not significant between the two aquaculture models, however there were significant differences of NH₄⁺-N, TN and TP fluxes at sediment-water interface. Otherwise, there was significantly positive relationship between nitrite and nitrate fluxes and DO concentration, while there was negative relationship between NH₄⁺-N and PO₄^3--P fluxes and DO concentration. Elevated temperature can promote different forms of nitrogen and phosphorus fluxes in aquacultural ponds.