Substance flow analyses (SFA) of phosphorus (P) have been examined on a national or supra-national level in various recent studies. SFA studies of P on the country scale or larger can have limited informative value; large differences between P budgets exist within countries and are easily obscured by country-wide average values. To quantify and evaluate these imbalances we integrated a country-scale and regional-scale model of the Danish anthropogenic P flows and stocks. We examine three spatial regions with regard to agriculture, as the main driver for P use, and waste management, the crucial sector for P recovery. The regions are characterised by their differences in agricultural practice, population and industrial density. We show considerable variation in P flows within the country. First, these are driven by agriculture, with mineral fertiliser inputs varying between 3 and 5 kg ha−1 yr−1, and animal feedstuff inputs between 5 and 19 kg ha−1 yr−1. We identified surpluses especially in areas with a larger proportion of animal husbandry, owing to additional application of manure in excess of crop P demand. However, redistribution of the large amounts of P in manure is not feasible owing to transport limitations. Second, waste management, closely linked to population and industrial density is the driver behind differences in recoverable P flows. Current amounts of potentially recoverable P cannot change the reliance on primary P. The most immediate P re-use potential exists in the areas around the eastern urban agglomerations, from more complete recovery of sewage sludge (with unrecovered P amounts of up to 33% of P in current mineral fertiliser imports) and the biowaste fraction in municipal solid waste currently not collected separately (24% of P in current mineral fertiliser imports), since this region shows both the highest proportion of crop production and fertiliser use and lowest soil P budget.