Regions with intensive agriculture often encounter environmental problems caused by nutrient excess of agro-food-waste systems that have become increasingly linear over previous decades. In this study, nitrogen (N), phosphorus (P), potassium (K) and carbon (C) flows in the whole agro-food-waste system of district Cleves in Germany were quantified simultaneously using substance flow analysis. Moreover, nutrient use inefficiency hotspots were identified to establish options to improve nutrient self-sufficiency as a first step towards nutrient circularity. Data on mass flows and nutrient contents was acquired for the year 2016 from stakeholders, statistical databases, literature and modelling. Organic C was included for flows with potential as organic fertilizer. Results show that animal production drives the nutrient flows in the export-oriented district, with feed import, manure application and losses from housing and manure storage accounting for 40, 45 and 60% of all N, P and K flows, respectively. In particular agriculture is responsible for N losses, with 150 kg N lost ha−1 agricultural land. Crop production surplus and with that soil accumulation of P and K are 515 t and 4100 t respectively. Stoichiometry of N:P:K:C in the different organic materials does not allow direct application and meeting crop requirements without exceeding demand of especially P. Processing of biomass is therefore required. Based on mass, especially manure holds potential for processing into bio-based fertilizers. To improve nutrient cycling and soil C conservation, being an important element for a sustainable agricultural sector, local balances between crop and animal production need to be considered.