Denmark has a long tradition of monitoring the aquatic environment. Previous monitoring has mainly focused on loss of nutrients and subsequent impacts on the biological structure in lakes and coastal areas. However, as part of the third Action Plan for the Aquatic Environment more emphasis has been put on stream ecology. The present paper describes background, strategy and content of the new NOVANA stream programme, which will run for the period 2004-2009. The new programme will encompass more than 800 stations covering all stream types in Denmark and monitoring will include three biological quality elements (macrophytes, macroinvertebrates and fish) as well as physico-chemical features and hydromorphological elements. In addition, the new programme integrates monitoring of elements both in the stream itself and in the riparian zone. Compliance with important European Commission Directives such as the Water Framework Directive and the Habitat Directive is discussed.