To sustain water-dependent economic and socio-ecological systems, natural capital and its interactions with other capitals is gaining attention, but a clear understanding of how to manage natural capital sustainably and how to make decisions relevant to water-related ecosystem services is yet to be achieved. In this study, we extended the framing of water-related ecosystem service flows as a cycle, integrating water quantity and quality and capturing the flows of ecosystem services (i.e., green phase) and ecosystem disservices (i.e., red phase), and connecting natural capital, built capital, and beneficiaries. We applied this framework to the Jiulong River watershed in China, using hydrological models to model water quantity and quality based on historical observations and experimental data. Our results showed that, during the green phase, the interactions of natural capital and built capital significantly improved water quality in downstream areas with higher flows. During the red phase, built capital reduced ecosystem disservices by ~10% while natural capital further reduced it by over one half. Our framework can provide information for natural capital management, eco-compensation, and pollutant management relevant to water-related ecosystem services.