.To control and prevent nutrient pollution from agricultural non-point sources, the Dutch government introduced the Mineral Accounting System (MINAS), a nutrient bookkeeping system which taxes farms with nutrient surpluses exceeding safe threshold values. Since the levies can be severe it is imperative to know what causes high nutrient surpluses. The large variation in surpluses is usually attributed to management factors like grazing, feeding and fertilising. Reducing surpluses is therefore assumed to be most effective through an improvement of management. Using technical and nutrient bookkeeping data of specialised dairy farms over 3 years (1997–1999) the effect of farm structure and farm management on nutrient surpluses is analysed with a partitioned linear regression model. Furthermore, the financial impacts are studied. The ratio between structure and management for the explanation of the nitrogen surplus was 1:3, and for phosphate 1:4 over the period 1997–1999. These ratios show that in current practices management is far more important than structure. Changing farm management rather than farm structure can therefore reduce nutrient surpluses more effectively, making it a more interesting approach for policy makers. Furthermore, improving management will also improve financial results.