Physico-chemical water quality in five of Spain's main rivers was assessed during the years 2001-2003. A previous physiographical river typology was carried out by applying System B of the Water Framework Directive (2000/60/CE) which distinguished four main river ecotypes: calcareous headwaters, siliceous rivers, plain rivers, and large rivers. The physiographical classification into river ecotypes also corresponded to distinct hydrochemical types. Reference values of ammonium, nitrate and phosphate fitted for local river ecotypes surpassed only slightly the natural and background levels established by the European Environmental Agency (EEA, 2003). Half of the sampled sites were above the limits established as reference conditions. Additionally, concentrations of ammonium, nitrite, nitrate, and phosphate increased when more percentage of land was dedicated to agriculture and less to forest land.