Water pollution is a serious problem in China. This study focuses on equality in pollution control in the Yangtze, Yellow and Pearl. We first quantified environmental targets for nitrogen (N) and phosphorus (P) at the river mouth. We used the Indicator for Coastal Eutrophication Potential and the Model to Assess River Inputs of Nutrients to seAs (MARINA) to project river export of nutrients. Next, we allocated the environmental targets to sub-basins as allowable levels, based on a Gini optimization approach. We searched for minimum inequality in pollution per unit of GDP, population, basin area, and agricultural area. Our results indicate that without pollution control, the river export of nutrients in 2050 exceed allowable levels. To meet the allowable levels while striving for equality, total dissolved N and P exports from sub-basins need to be reduced by 60 to 97%. The required reductions are largest for sub-basins of the Yellow River. For P, reducing point source inputs to rivers (manure and sewage) may be enough to avoid that allowable levels are exceeded in many sub-basins. For N, more needs to be done. Some sub-basins need to reduce their pollution more than others. Equality considerations call for reducing both point (e.g. recycling manure resources on the land) and diffuse (improve nutrient use efficiencies in agriculture) sources of N in the rivers. Our study is the first to link a Gini based optimization approach with the MARINA model. It may support decision making aimed at cleaner production and at equality in pollution control.