As the first pilot provincial water environmental compensation set up at the national level, the Xin’anjiang River Basin plays a very important exemplary and guiding role in the ecological compensation of transboundary basins in China. There is no paper evaluating the environmental performance in watershed scale after getting rid of the natural factor’s effect. Here we issue a new approach to evaluate it, combing the SPAtially Referenced Regression On Watershed attributes (SPARROW) models and data envelopment analysis (DEA) method, based on counterfactual scenarios. After ecological compensation, the results show that the decrease of total nitrogen (TN) non-point source export coefficient was stable (17.16–17.78% in different sources), while that of total phosphorus (TP; 8.51–17.75%) and permanganate index (COD_Mn; 13.10–21.41%) was not. The projects of fertilizer application’s effects were relatively obvious; on average, the decreases of the export coefficients were 17.16%, 17.75%, and 21.41% in TN, TP, and COD_Mn models, respectively, showing the importance of eco-compensation regulation, not only in non-point source pollution reduction but also resulting in high levels of eco-compensation efficiencies, especially in scale efficiencies. By assessing parameter and modeling uncertainty with the use of the generalized likelihood uncertainty estimation (GLUE) method, the models’ structure well represents the hydrological behavior. This study also provides policymakers with a new perspective in accurately measuring the impact of environmental performance, to guide the next step of environmental investment optimization.

Ammonium nitrogen (NH₄⁺-N), which naturally arises from the decomposition of organic substances through ammonification, has a tremendous influence on local water quality. Therefore, it is vital for water quality protection to assess the amount, sources, and streamflow transport of NH₄⁺-N. SPAtially Referenced Regressions on Watershed attributes (SPARROW), which is a hybrid empirical and mechanistic modeling technique based on a regression approach, can be used to conduct studies of different spatial scales on nutrient streamflow transport. In this paper, the load and delivery of NH₄⁺-N in Poyang Lake Basin (PLB) and Haihe River Basin (HRB) were estimated using SPARROW. In PLB, NH₄⁺-N load streamflow transport originating from point sources and farmland accounted for 41.83% and 32.84%, respectively. In HRB, NH₄⁺-N load streamflow transport originating from residential land and farmland accounted for 40.16% and 36.75%, respectively. Hence, the following measures should be taken: In PLB, it is important to enhance the management of the point sources, such as municipal and industrial wastewater. In HRB, feasible measures include controlling the domestic pollution and reducing the usage of chemical fertilizers. In addition, increasing the vegetation coverage of both basins may be beneficial to their nutrient management. The SPARROW models built for PLB and HRB can serve as references for future uses for different basins with various conditions, extending this model’s scope and adaptability.