Optimization of conjunctive water use in hydro-systems considering quality constraints, due to the complexity of the resulting nonlinear problem solution, are addressed within a short-term horizon by researchers. In this research, an optimizing model was proposed for long-term conjunctive use of water at the basin that maximizes the hydro-system operation reliability and considers TDS as a water quality index. In the proposed model, by the use of model decomposition and aggregation among different parts of the model, and developing a linearizing algorithm, modeling and analysis of large hydro-systems (at the basin scale) within a long-term horizon is provided so that the water quantity and quality deficits are minimized. Results of model application to Zayandehrud watershed in a thirty year period (2001-2030) showed the improvement of water quality at the Gavkhuni wetland up to 50% in dry and high demand months. Model prescribed operational rules have supplied water demands with 68% reliability along the Zayandehrud River. Model application to Zayandehrud hydro-system shows a meaningful improvement in the water supply with suitable quality in the river for agricultural and environmental demands. However, more detail of this improvement must be determined by other models that operate in smaller spatial and temporal scale, based on the results of the presented long-term model in this study.