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Livestock manure and food waste are major contributors to nutrient pollution, greenhouse gas (GHG) emissions, and environmental degradation across agricultural and urban landscapes. In livestock-dominated regions, repeated manure application often exceeds local crop uptake capacity, creating spatially concentrated nitrogen (N) and phosphorus (P) surpluses that disproportionately drive eutrophication and diffuse nutrient losses to surface waters. At the same time, these organic waste streams represent an underutilized resource for renewable energy and nutrient recycling. Anaerobic digestion (AD) offers a pathway to address these coupled challenges by converting organic residues into renewable natural gas (RNG) while producing nutrient-rich digestate that can partially replace synthetic fertilizers. However, the water-quality, climate, and energy benefits of AD are rarely realized in practice because manure and food waste are spatially mismatched, transport costs are high, and infrastructure is typically deployed through ad hoc, facility-level decisions rather than coordinated, landscape-scale planning.To address these barriers, we developed SYNERGI (SYstemic Nutrient and Energy Recovery through Geo-Informed Integration), a high-resolution techno-economic spatial optimization framework that integrates organic waste availability, transport logistics, digester scaling, costs, and environmental co-benefits. Applied to Ontario, Canada, SYNERGI demonstrates that system-level design strongly governs trade-offs across nutrient pollution control, GHG mitigation, and energy recovery. An energy-maximizing configuration produces RNG at an unviable cost of $45.4 GJ⁻¹, whereas cost-optimized systems reduce average production costs to $16.3 GJ⁻¹ while shrinking infrastructure requirements from 668 digesters to just 82 strategically located facilities.The framework reveals pronounced spatial heterogeneity driven by feedstock composition and accessibility: manure-only systems in remote livestock regions face high costs and persistent nutrient pressure, whereas co-digesting facilities near urban food-waste sources achieve substantially lower costs and greater opportunities for nutrient redistribution. By weakening extreme nutrient surplus hotspots and realigning nutrient supply with crop demand, optimized biogas deployment reduces the likelihood and severity of nutrient over-application, even when total nutrient inputs are conserved. Together, these results illustrate how spatially informed planning tools can support integrated strategies that simultaneously advance water-quality protection, climate mitigation, and renewable energy goals within the water–food–energy–environment nexus.