The Netherlands is one of the most densely populated countries in terms of people and livestock and is the second largest exporter of agricultural products worldwide. As a result, the Netherlands has a manure surplus. Excess application of manure can lead to environmental problems; therefore, manure needs to be treated and discharged. Manure can contain zoonotic pathogens, but whether exposure to manure and manure treatment also poses a risk to public health is still unknown. This study analysed the regulations, relevant actors, and responsibilities in the complex system of manure and public health in the Netherlands. Interviews and system mapping have demonstrated interlinkages between environmental, economic, and health aspects. Constraints and opportunities for public health protection have been identified. This study reveals the complexity of the Dutch manure policy, its scattered responsibilities, the challenge to deal with uncertainties, and, most importantly, the need for a microbial risk assessment in order to adequately communicate and manage possible risks to protect the health of animals, the environment, and people.