Agricultural systems are the greatest consumers of freshwater in the world and irrigation return flows are one of the main pollutants of water bodies. This paper analyzes the hydrologic dynamics and water quality (salinity and nitrate concentrations) of an aquifer belonging to a traditional irrigated land. The study was carried out for the hydrologic years of 2006, 2007 and 2008, relating changes in water quality with geological and agricultural characteristics of the evaluated irrigated land. The study reveals that the surface hydrological basin and groundwater hydrological basin do not coincide, so a contribution from the aquifer recharge by groundwater flow was added to the aquifer recharge by water drainage from the surface basin. Regarding water quality, 4% of the collected samples exceeded the value limit established for waters intended for irrigation (3.0 dS/m) and human consumption (2.5 dS/m). Concerning nitrates, 35% of the collected samples exceeded the 50 mg NO3 -/l limit established for waters intended for human consumption and 33% exceeded the control range 25-50 mg NO3 -/l. There were significant differences between water samples collected during the irrigation period, as a consequence of leaching evapoconcentrated salts and the good quality of the water used for irrigation. Concerning spatial distribution, water quality in the aquifer is related to the quality of groundwater flow, drainage from surface basin, seepage from irrigation canals, subsurface salt dissolution and leaching of nitrogen fertilizers. Nitrate is the main environmental problem, requiring further studies to evaluate alternatives to minimize nitrate pollution.