The loss of agricultural pollutants through drainage can be related to the irrigated land of the hydrological basin and therefore it is possible to establish a legislation based on maximum allowed values of pollutant exported loads. As a continuation of the evaluation of water use, this second part of the study evaluates the contamination induced by the 59.200 ha of irrigated land in the Bardenas irrigation district, which belongs to the Arba basin. Mass balances (salt and nitrate) were accomplished, assigning concentration values to each one of the water balance components in the period 2004-2007. The Salt Contamination Index (ICS) and the Nitrate Contamination Index (ICN) were analyzed; these indices correct the unitary mass of pollutants exported by the salinity and fertilization needs of the studied irrigated land. The ICS and ICN decreased, respectively, 15% and 23% from 2004 to 2007, as an effect of the drainage water reuse, these indices presented values 60% lower than the ones obtained in small basins of the same Irrigation District. The ICS values were similar to the new irrigation lands with good management, but the ICN values were 24% higher. The results showed little possibilities to reduce the salt contamination as well as the necessity to adequate the combination of irrigation and fertilization management, as a way to minimize the nitrates pollution. This will not be easy to achieve in Bardenas because of the presence of inadequate soils for flood irrigation, which does not allow sufficient control of the application of water and nitrogen.