Salinity contamination caused by irrigation has been widely studied but the analysis of geochemical processes regarding agronomic variables has not adequately been considered yet. The research presented here analyzes the influence of changes in irrigation management on salinity contamination, through the use of geochemical modeling techniques, in an agricultural basin during the hydrological year of 2001 and within the period 2005-2008. The results indicate that the changes implemented in irrigation management reduced the masses of salts exported in 72%, although water salinity increased by 25% (this salinity level does not restrict its use for irrigation). The different ionic ratios in drainage water, the results of the salinity balances, and the results of geochemical calculations (mass balances and speciation-solubility) indicate, mainly, precipitation of calcite, dissolution of gypsum and halite and cation exchange. The salt contamination index decreased from approximately 70% to levels close to those presented in modern irrigation areas, indicating that the changes in irrigation management were effective. Petrocalcic genesis and punctual sodification of soils can constitute an agroenvironmental problem that requires adequate management of irrigation and drainage considering future modernization of irrigation areas.