Integrated shrimp-rice systems have been widely applied in paddy fields around the world but have never been constructed in brackish water ponds. In this study, two types of rice cultivars and three shrimp varieties with different salinity requirements were cocultured in two freshwater ponds (local rice-Litopenaeus vannamei and local rice-Macrobrachium rosenbergii) and two brackish water ponds (sea rice-Litopenaeus vannamei and sea rice-Penaeus monodon) under practical shrimp farming conditions. The nutrient removal ability and water stability of these four integrated systems were tested by comparing the nutrient concentrations and water parameters with those of shrimp monoculture ponds. The rice and shrimp varieties alone and their interaction had differential effects on the studied parameters. The results showed that dissolved nitrogen (ammonia-N, nitrate-N and nitrite-N), phosphorus concentration and COD_Mn in shrimp-rice ponds were significantly lower than those in shrimp monoculture ponds, with reductions of 74.32%, 76.29%, 85.57%, 35.93% and 10.64%, respectively. Nitrate-N was significantly lower (55.88%) in the sea rice pond than in the local rice ponds. The nutrient content in monoculture ponds changed dramatically over time, especially during the middle and late stages of breeding, but was relatively stable in shrimp-rice ponds without extreme values occurring for any analyzed water parameters. The results of this study suggested that integrated shrimp-rice pond culture was an effective method to improve nutrient utilization efficiency and helped to illustrate the potential applications of integrated brackish water shrimp-rice models in coastal areas of China and other countries.