Waste load allocation (WLA), as a well-known total pollutant control strategy, is designed to distribute pollution responsibilities among polluters to alleviate environmental problems, but the current policy is unfair and limited to single scale or single pollution types. In this paper, a new, alternative, multi-scale, and multi-pollution WLA modeling framework was developed, with a goal of producing optimal and fair allocation quotas at multiple scales. The new WLA modeling framework integrates multi-constrained environmental Gini coefficients (EGCs) and Delphi-analytic hierarchy process (Delphi-AHP) optimization models to achieve the stated goal. The new WLA modeling framework was applied in a case study in the Xian-jiang watershed in Zhejiang Province, China, in order to test its validity and usefulness. The results, in comparison with existing practices by the local governments, suggest that the simulated pollutant load quota at the watershed scale is much fairer than the existing policies and even has some environmental economic benefits at the pollutant source scale. As the new WLA is a process-based modeling framework, it should be possible to adopt this approach in other similar geographic areas.