NENUPHAR tackles one of Europe’s most persistent environmental and economic challenges: excess Nitrogen and Phosphorus from agriculture and wastewater. These nutrients degrade soils, waters and air, while valuable nutrients in manure, sewage sludge and dairy effluents remain underused. The project aims to turn these waste streams into safe, locally reusable resources and reduce diffuse pollution at basin scale. The main objective is to prove, in real settings, that integrated solutions combining governance reform, policy instruments and mature technologies can both prevent N/P emissions and recover nutrients for farming. NENUPHAR works through multi-actor regional clusters that map nutrient flows, co-design governance arrangements and test enabling technologies. These technologies include ammonia stripping for manure, safe composting routes for sludge, membrane and pre-oxidation treatments, and nature-based system with ultrasounds operations for water dairy. It provides authorities, utilities and farmers gain trusted performance, cost and safety evidence. This approach is anchored in three lighthouse river basins with distinct pressures and governance contexts: the Ebro (intensive livestock and irrigation dynamics), the Lielupe (diffuse agricultural loads in a lowland catchment) and the Danube (large transboundary system with mixed urban–rural sources), which together offer robust, transferable lessons. Two replication sites: Bornholm and Cyprus, extend the use cases to island settings characterised by seasonal demand peaks, water scarcity, limited land for manure/sludge handling and high fertiliser import dependence, demonstrating how solutions can be adapted where infrastructure and logistics constraints are more severe. The project combines life-cycle and techno-economic assessments with business models and replication roadmaps. Social sciences are embedded throughout, including stakeholder and network analysis, behavioural insights, and co-created incentives and regulatory pathways. NENUPHAR’s route to impact is clear: measurable reductions in nutrient losses and air emissions, increased regional nutrient autonomy, new revenue streams for waste and wastewater managers, and more resilient farming systems that rely less on imported fertilisers. These outcomes support environmental quality and rural competitiveness across the EU.