Local-scale opportunities to address challenges of the water-food nexus in the developing world need to be embraced. Borehole-garden permaculture is advocated as one such opportunity that involves the sustainable use of groundwater spilt at hand-pump operated borehole supplies that is otherwise wasted. Spilt water may also pose health risks when accumulating as a stagnant pond. Rural village community use of this grey-water in permaculture projects to irrigate borehole gardens is proposed to primarily provide economic benefit whereby garden-produce revenue helps fund borehole water-point maintenance. Water-supply sustainability, increased food/nutrition security, health protection from malaria, and business opportunity benefits may also arise. Our goal has been to develop an, experience-based, framework for delivery of sustainable borehole-garden permaculture and associated benefits. This is based upon data collection and permaculture implementation across the rural Chikwawa District of Malawi during 2009-17. We use, stakeholder interviews to identify issues influencing uptake, gathering of stagnant pond occurrence data to estimate amelioration opportunity, quantification of permaculture profitability to validate economic potential, and critical assessment of recent permaculture uptake to identify continuing problems. Permaculture was implemented at 123 sites representing 6% of District water points, rising to 26% local area coverage. Most implementations were at, or near, newly drilled community-supply boreholes; hence, amelioration of prevalent stagnant ponds elsewhere remains a concern. The envisaged benefits of permaculture were manifest and early data affirm projected garden profitability and spin-off benefits of water-point banking and community micro-loan access. However, a diversity of technical, economic, social and governance issues were found to influence uptake and performance. Example issues include greater need for improved bespoke garden design input, on-going project performance assessment, and coordinated involvement of multi-sector governmental-development bodies to underpin the integrated natural-resource management required. The developed framework aims to manage the identified issues and requires the concerted action of all stakeholders. Based on the probable ubiquity of underlying issues, the framework is expected to be generalizable to the wider developing world. However, this particular application of permaculture represents a fraction of its greater potential opportunity for rural communities that should be explored.