The separation between crop- and livestock production is an important driver of agricultural nutrient surpluses in many parts of the world. Nutrient surpluses can be symptomatic of poor resource use efficiency and contribute to environmental problems. Thus, it is important not only to identify where surpluses can be reduced, but also the potential policy tools that could facilitate reductions. Here, we explored linkages between livestock production and nutrient flows for the Baltic Sea catchment and discuss management practices and policies that influence the magnitude of nutrient surpluses. We found that the majority of nutrients cycled through the livestock sector and that large nitrogen and phosphorus surpluses often occurred in regions with high livestock density. Imports of mineral fertilizers and feed to the catchment increased overall surpluses, which in turn increased the risk of nutrient losses from agriculture to the aquatic environment. Many things can be done to reduce agricultural nutrient surpluses; an important example is using manure nutrients more efficiently in crop production, thereby reducing the need to import mineral fertilizers. Also, existing soil P reserves could be used to a greater extent, which further emphasizes the need to improve nutrient management practices. The countries around the Baltic Sea used different approaches to manage agricultural nutrient surpluses, and because eight of the coastal countries are members in the European Union (EU), common EU policies play an important role in management. We observed reductions in surpluses between 2000 and 2010 in some countries, which suggested the influence of different approaches to management and policy and that there are opportunities for further improvement. However, the separation between crop and livestock production in agriculture appears to be an underlying cause of nutrient surpluses; thus, further research is needed to understand how policy can address these structural issues and increase sustainability in food production.