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Land application of secondary industrial effluent to Chihuahuan Desert upland near Las Cruces, New Mexico, was designed to meet the water demand of creosote and mesquite shrubs. The major objective of this study was to assess changes in chemical and physical properties of desert soils after 4 years (2002-2005) of irrigation with secondary industrial effluent. Soil texture and bulk density (pb) did not differ between irrigated and control plots, but did so between bare ground and mesquite sites in the control and irrigated plots. Reductions in saturated hydraulic conductivity (Ks), drainable porosity (d), and effective porosity (e) in the upper 0-15cm of irrigated plot soils were attributed to decline of soil structure and dispersion of clays resulting from the addition of highly sodic and alkaline effluent to irrigated plots. Although rarely significant, consistently higher electrical conductivity, sodium adsorption ratio, chloride, exchangeable sodium percentage, and Na+ in the soil profile (between 30cm and 210cm) at creosote and mesquite sites compared to the bare ground site suggested deeper leaching of wastewater constituents at shrub sites. Deeper leaching of wastewater constituents beneath shrubs compared to bare ground areas may be attributed to higher water inputs caused by sprinkler spray interception, and higher Ks, d, and e of soils beneath creosote and mesquite canopies. Continued application of industrial effluent to a Chihuahuan Desert ecosystem over the long term should consider the relative importance of canopy and intercanopy areas.