Increasing human populations are placing greater strain on water resources, prompting the use of treated wastewater effluent for irrigation in some areas, including the desert regions of the Western United States. To determine the potential effects of using secondary effluent for irrigation, we applied wastewater effluent and irrigation waters to natural and artificially constructed calcareous soils in greenhouse and field lysimeters, and in soil columns. The leachate from one field lysimeter contained increased fecal coliform counts than the effluent. Leachate coliform counts were decreased or not significantly changed in two field lysimeters. Electrical conductivity (EC), sodium adsorption ratio (SAR), chloride and nitrate concentrations also increased significantly in the leachate of the three field lysimeters however. Samples collected from the greenhouse lysimeters showed a significant decrease in all categories except EC, was not significantly changed. Soil column drainage samples showed a decrease in coliform counts, and increase in EC and chloride levels while SAR and nitrate levels varied with clay content. Preferential flow of coliform bacteria and high EC and SAR values could indicate long term effects that may affect the sustainability of the practice.