In this paper, a new methodology is developed for integrated allocation of water and waste-loads in river basins utilizing a fuzzy transformation method (FTM). The fuzzy transformation method is used to incorporate the existing uncertainties in model inputs. In the proposed methodology, the FTM, as a simulation model, is utilized in an optimization framework for constructing a fuzzy water and waste-loads allocation model. In addition, economic as well as environmental impacts of water allocation to different water users are considered. For equitable water and waste load allocation, all possible coalition of water users are considered and total benefit of each coalition, which is a fuzzy number, is reallocated to water users who are participating in the coalition. The fuzzy cost savings are reallocated using a fuzzy nucleolus cooperative game and the FTM. As a case study, the Dez River system in south-west of Iran is modeled and analyzed using the methodology developed here. The results show the effectiveness of the methodology in optimal water and waste-loads allocations under uncertainty.