Worldwide, nitrogen (N) and phosphorus (P) losses from agriculture are main contributors to eutrophication of water bodies so that forceful agro-technical measures are required to reduce their diffuse discharge to the environment. With view to worldwide finite mineral rock phosphates efficient standards are required to close the agricultural P cycle. In intensive agricultural livestock production manure is often treated as a waste problem rather than an organic fertilizer and source of nutrients. Consequently, application rates of manure are not based on a documented demand of nutrients, but fully exhaust the maximum legal output quantity. However, even if maximum manure loads will not exceed an upper limit of 170 kg/ha N, its use is not sustainable as it exceeds the mean P off-take of 22 kg/ha P by agricultural crops with harvest products by 95% to >120% if pig and poultry manure are applied. A solution to the problem offers the limitation of manure rates on basis of P loads that equal the off-take. This simple math stresses the urgent need to revise current practices of manure application and to focus on innovations in the production and recycling chain of manure and slurries. In general, the implementation of Codes of Good Agricultural Practice (GAP) on farms is recommended to reduce the pollution from agricultural activities. Variable rate application of fertilizers complies with GAP codes as it matches the small-scale variation of plant available nutrients in soils with the nutrient demand of crops. It is intrinsic that such site-specific nutrient management complies with a sustainable input of resources that favors crop growth and minimizes negative impacts on the environment. Algorithms for the continuous variable rate input of straight and compound mineral fertilizers, and farmyard manure have been developed. The present contribution demonstrates the problem of P accumulation in soils of livestock farms, addresses the spatial variation of plant available P in soils, and provides algorithms for a balanced, variable rate fertilization of manure.