River water pollution is of major concern in agricultural watersheds. In Europe, the introduction of the Water Framework Directive in 2000, binds obligations on member states to achieve good ecological status of surface water and groundwater by 2015. Non-point pollution takes place in river waters after agricultural irrigation through surface runoff, lateral and groundwater flows, in relation with agricultural practices and soil, and geomorphologic and meteorological characteristics of the watershed. This work was investigated in the Flumen watershed (1,500 km², in Monegros region in Aragon, Northeastern of Spain), an agricultural watershed located in semi-arid environment, and was supported by the EU AguaFlash project (http://www.aguaflash-sudoe.eu/). In this watershed, agricultural use corresponds to an intensive irrigation for cereal, maize, rice and alfalfa production. The SWAT model (2009 version) has been applied from October 2009 to March 2011. Daily time step was used to assess the flux and transport of nitrates, suspended sediments and pesticides. Simulated concentrations were compared to data collected at the watershed outlet with weekly measurements during low flow and daily or subdaily measurements during flood events. Low water during summer period in the Flumen watershed is controlled by the drainage of water used in agriculture lands for irrigation. Consequently, nitrate and soluble pesticide concentrations were diluted during flood events. Annual transfer shows a low correlation with watershed annual water yields. Suspended sediments were transported during flood events with some pesticides associated to the particles.