A budget allocation system for regional water quality management to achieve environmental sustainability was developed in this study to assist a local authority with making appropriate budget allocations for improving Regional Water Environmental Sustainability (RWES) in an efficient manner. The system consists of visions and goals, RWES indicators, and an analysis of budget allocation versus RWES. Visions and goals define task priorities for improving water environmental sustainability. Indicators are used to measure the progress of related tasks toward RWES goals. These indicators are classified by the Driving Force-State-Response (DSR) framework to facilitate the analysis of relationships among indicators. Linkages between budget allocation and indicators are also analyzed, and the result is used to assess whether the available budget is allocated properly to raise the RWES. The applicability of the system is demonstrated by a case study involving a local environmental protection authority.