Excessive amounts of nutrients in rivers promote biological growth of periphyton and macrophytes to nuisance levels. Of most concern, because they are immediately available for growth, are dissolved inorganic forms of nitrogen (N) and phosphorus (P), primarily as nitrate-N and dissolved reactive phosphorus (DRP). To help understand the sources of dissolved nutrients, we estimated and mapped subsurface flow (i.e. leaching) losses of nitrate and DRP. There are large areas of high nitrate leaching in Waikato, Bay of Plenty, Taranaki and Canterbury. The high spatial detail of the maps permits use for planning mitigation at local, regional and national scales. However, they should not be used to infer leaching rates for particular farms as average farming practices are assumed. The nitrate leaching maps were driven primarily by animal numbers, so regional trends of total leached nitrate between 1990 and 2010 were able to be determined from regional statistics of farm animals.