Pollution of ground-and surface waters with nitrates from agricultural sources poses a risk to drinking water quality and has negative impacts on the environment. At the national scale, the gross nitrogen budget (GNB) is accepted as an indicator of pollution caused by nitrates. There is, however, little common EU-wide knowledge on the budget application and its comparability at the farm level for the detection of ground-and surface water pollution caused by nitrates and the monitoring of mitigation measures. Therefore, a survey was carried out among experts of various European countries in order to assess the practice and application of fertilization planning and nitrogen budgeting at the farm level and the differences between countries within Europe. While fertilization planning is practiced in all of the fourteen countries analyzed in this paper, according to current legislation, nitrogen budgets have to be calculated only in Switzerland, Germany and Romania. The survey revealed that methods of fertilization planning and nitrogen budgeting at the farm level are not unified throughout Europe. In most of the cases where budgets are used regularly (Germany, Romania, Switzerland), standard values for the chemical composition of feed, organic fertilizers, animal and plant products are used. The example of the Dutch Annual Nutrient Cycling Assessment (ANCA) tool (and partly of the Suisse Balance) shows that it is only by using farm-specific “real” data that budgeting can be successfully applied to optimize nutrient flows and increase N efficiencies at the farm level. However, this approach is more elaborate and requires centralized data processing under consideration of data protection concerns. This paper concludes that there is no unified indicator for nutrient management and water quality at the farm level. A comparison of regionally calculated nitrogen budgets across European countries needs to be interpreted carefully, as methods as well as data and emission factors vary across countries. For the implementation of EU nitrogen-related policies—notably, the Nitrates Directive—nutrient budgeting is currently ruled out as an entry point for legal requirements. In contrast, nutrient budgets are highlighted as an environment indicator by the OECD and EU institutions.