Nitrate leaching is a common problem in frequently fertilized agricultural crops in Southern New Mexico. The objectives of this study were to estimate the leaching depths, irrigation and plant uptake efficiencies for onion (Allium cepa L.), chile (Capsicum annuum), and cotton (Gossypium spp.) crops. The study aims to determine how existing best management practices for these three specialty crops could be improved. Soil samples collected monthly for two growing seasons starting April 2007 to June 2010 were analyzed for NO3-N and chloride concentrations. The NO3-N loadings below the rooting zone varied from 22 to 92kgha−1 during growing season 1 and 18–90kgha−1 during growing season 2 in all the three experimental fields. The leaching fractions (LFs) varied from 0.09 to 0.21 during growing season 1 and 0.08–0.22 during growing season 2 in the experimental fields. The irrigation efficiencies (IE=1−LF) ranged from 79 to 91% during growing season 1 and from 78 to 92% during growing season 2 in all the three fields. Nitrogen application efficiencies (NAEs) varied from 39 to 75% during growing season 1 and 40–76% during growing season 2 in all the experimental fields. Under the prevalent management conditions, cotton field showed higher irrigation efficiency as well as the NAE as compared to onion and chile fields. Based on the soil N content at the end of growing seasons, the results indicate that reducing fertilizer applications until bulb formation in onions and flower initiation in chile can decrease the amount of fertilizer applications to as much as half, thus can help in reducing the NO3-N leaching and improving nitrogen and water efficiencies.