Despite the billions of euros used as subsidies over recent decades, Portugal’s water sector continues to struggle, being characterized by significant inefficiencies and differences between high- and low-performing water and sanitation services (WSSs). Current subsidy policies lack transparency and are not linked to performance results, undermining efforts to promote efficiency and sustainability in both environmental and financial dimensions. To address these issues, this article highlights relevant aspects to be taken into account in the redefinition of funding allocation in the Portuguese WSS sector. By implementing performance-based criteria for subsidy allocation and prioritization, regardless of the identity of beneficiaries or providers, we aim to instigate accountability and efficiency in this process. The analysis draws on empirical data to highlight the shortcomings of existing practices and demonstrates the potential benefits of adopting the “user-pays” principle. This principle is able to improve the definition of tariffs aiming for full cost recovery, while still providing for disadvantaged and vulnerable customers through social tariffs or assistance programs. Key findings indicate that coordinated efforts among government agencies, regulators, public and private utilities, and municipalities are essential to develop and promote effective financing strategies. This stakeholder’s cooperation is essential for managing the urban water cycle sustainably and addressing the sector’s long-term challenges. This research implies that a strategic shift in subsidy allocation is required, to develop accountability, efficiency, and equity in the WSS sector. The allocation of financial resources must be better justified to enhance overall performance in the sector.