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Nature-based solutions (NbS) are widely promoted to enhance water security. However, their implementation can generate trade-offs that, if overlooked, risk undermining long-term sustainability and equity. As NbS are scaled up, decision-makers require approaches that can anticipate not only benefits, but also disbenefits, who bears them, and how coupled socio-environmental systems respond to interventions over time. Without such perspectives, NbS may achieve short-term gains while failing to function effectively or equitably in the long run.Here, we use a participatory systems modelling approach to examine NbS planning in the water supply region of Lima, Peru (the rural-urban CHIRILUMA system), where ecosystem conservation and ancestral infiltration-enhancement infrastructure are being implemented through initiatives such as the national Mechanism of Reward for Ecosystem Services (MRSE). The analysis reveals synergies and tensions between ecological, economic, and social objectives—such as between ecosystem health and rural livelihoods—and shows how isolated responses to these tensions can trigger feedbacks that undermine NbS performance.We extend the conceptual systems analysis through semi-quantitative simulations that compare NbS implementation strategies. These simulations enable assessment of how trade-offs and feedbacks evolve over short- and long-term horizons, how benefits and disbenefits are distributed, and when NbS interventions risk losing effectiveness or reinforcing inequities. Framing these outcomes as potential system failures allows us to identify leverage points to manage trade-offs, including the alignment of local practices with institutional arrangements and the strengthening of mechanisms for long-term maintenance and benefit sharing.Overall, the study demonstrates how systems-based approaches can support NbS planning that anticipates system responses, reduces the risk of system failures, and promotes more robust and equitable water management in complex, high-risk settings.