The lack of generic methods to assess the environmental consequences of agricultural practices and the lack of consensus on monitoring and evaluation of environmental, agricultural and socio-economic effects of agri-environment schemes (AES) in EU Member States call for better evaluation methods. The ‘Agri-environmental Footprint’ project proposed to deal with these problems by establishing a new evaluation method, the Agri-Environmental Footprint Index (AFI). The AFI is an index customised to local stakeholder preferences, using expert knowledge for assessment of impacts and sensitivity, and indicators of the environmental state at farm level. In a Danish test case, agricultural practices at twenty-five farms in two groundwater protection zones were assessed. Data was collected from databases, registers, maps and interviews with farmers. The index was calculated for 1996/7 and 2006/7 to track temporal development and effects of entering an agri-environmental scheme. The Danish case demonstrated that the index can be used to track changes in environmental impacts and that entering agri-environmental scheme had a positive impact on the index value. However, the index should be used with caution. It is important to consider the robustness of each indicator: to assess whether changes will occur over time; whether changes are linked to management practices or external factors; and whether data are available up to date. Indicators dependent upon uptake data from agri-environmental schemes should be used with great caution. Retrospective use of stakeholder preferences is subject to uncertainty because preferences may have changed over time.